Population structure and gene flux of Listeria monocytogenes ST121 reveal prophages as a candidate driver of adaptation and persistence in food production environments

Background

Listeria monocytogenes is a bacterial pathogen found in an increasing number of food categories, potentially reflecting an expanding niche and food safety risk profile. In the United Kingdom, L. monocytogenes sequence type (ST) 121 is more frequently isolated from foods and food environments than from cases of clinical listeriosis, consistent with a relatively low pathogenicity. In this study, we determined the microevolution associated with the environmental persistence of a L. monocytogenes clone by investigating clone-specific genome features in the context of the ST121 population structure from international sources. To enable unambiguous comparative genomic analysis of ST121 strains we constructed 16 new high-quality genome assemblies from L. monocytogenes isolated from foods, food environments, and human-clinical sources in the UK from 1987 to 2019.

Genome assemblies

Hybrid assemblies of strains 07-032, BL87-028, BL89-019, BL89-020, 399454, 246242, 163381, 241745, 457441, 389690, 535305, 396044, 246255, 259390, 754322 and 757923 were produced using long and short reads. Long reads were adapter trimmed with Porechop v0.2.3 and filtered with filtlong v0.2.1 to keep the 95% of the best reads longer than 6000 bp. Contamination of the filtered reads was assessed using kraken2 v2.1.1 against the kraken2 database Standard. A long-read assembly was produced using the filtlong filtered reads as input to the Flye assembler v2.7 with the nano-raw mode. Long reads were filtered again with filtlong to keep reads longer than 1000 bp, and the resulting reads were used to polish the circular long-read assemblies using medaka v1.4.3. Paired-end short reads were filtered with trimmomatic v0.38.0 using default parameters with a sliding window of 4 bp and quality of 20 and inspected for contamination using kraken2 v2.1.1. The long-read assembly was further polished with the filtered short reads using pilon v1.24 with the following nextflow script.

Using default parameters, Fastq files from strains 1537877 and 1594542 underwent trimming using TrimGalore v0.4.3. Next, the quality of the resulting paired-end sequences was assessed using FastQC v0.11.8, sequences were filtered based on a GC content above 39% and N bases in a proportion higher than 5%. Assemblies were constructed using shovill v1.1.0 with SPAdes v3.14 as assembler.

Assemblies of strains H094800054 and 130 were downloaded from the Institute Pasteur's BIGSdb on 22 September 2022.

Genomes were annotated using Bakta v1.6.1.

Files 

File 07_032.fsa corresponds to the hybrid assembly of L. monocytogenes strain 07-032 and annotations are in file 07_032.gff3File BL87_028.fsa corresponds to the hybrid assembly of L. monocytogenes strain BL87-028 and annotations are in file BL87_028.gff3File BL89_019.fsa corresponds to the hybrid assembly of L. monocytogenes strain BL89-019 and annotations are in file BL89_019.gff3File BL89_020.fsa corresponds to the hybrid assembly of L. monocytogenes strain BL89-020 and annotations are in file BL89_020.gff3File 163381_SRR6807418.fsa corresponds to the hybrid assembly of L. monocytogenes strain 163381 and annotations are in file 163381_SRR6807418.gff3File 399454_SRR7163869.fsa corresponds to the hybrid assembly of L. monocytogenes strain 399454 and annotations are in file 399454_SRR7163869.gff3File 241745_SRR7167591.fsa corresponds to the hybrid assembly of L. monocytogenes strain 241745 and annotations are in file 241745_SRR7167591.gff3File 457441_SRR7827106.fsa corresponds to the hybrid assembly of L. monocytogenes strain 457441 and annotations are in file 457441_SRR7827106.gff3File 389690_SRR7841399.fsa corresponds to the hybrid assembly of L. monocytogenes strain 389690 and annotations are in file 389690_SRR7841399.gff3File 246242_SRR7850130.fsa corresponds to the hybrid assembly of L. monocytogenes strain 246242 and annotations are in file 246242_SRR7850130.gff3File 535305_SRR7866357.fsa corresponds to the hybrid assembly of L. monocytogenes strain 535305 and annotations are in file 535305_SRR7866357.gff3File 396044_SRR7866629.fsa corresponds to the hybrid assembly of L. monocytogenes strain 396044 and annotations are in file 396044_SRR7866629.gff3File 246255_SRR7873592.fsa corresponds to the hybrid assembly of L. monocytogenes strain 246255 and annotations are in file 246255_SRR7873592.gff3File 259390_SRR7873684.fsa corresponds to the hybrid assembly of L. monocytogenes strain 259390 and annotations are in file 259390_SRR7873684.gff3File 754322_SRR9226492.fsa corresponds to the hybrid assembly of L. monocytogenes strain 754322 and annotations are in file 754322_SRR9226492.gff3File 757923_SRR9298670.fsa corresponds to the hybrid assembly of L. monocytogenes strain 757923 and annotations are in file 757923_SRR9298670.gff3

File 1838_H094800054.gff3 corresponds to the annotation of the draft assembly of L. monocytogenes strain H094800054File 79394_130.gff3 corresponds to the annotation of the draft assembly of L. monocytogenes strain 130File 1537877_SRR17120467.gff3 corresponds to the annotation of the draft assembly of L. monocytogenes strain 1537877File 1594542_SRR18333768.gff3 corresponds to the annotation of the draft assembly of L. monocytogenes strain 1594542

File All_pangenome_reference.fa corresponds to the pangenome sequences of 482 L. monocytogenes strains of ST121File Chr_pangenome_reference.fa corresponds to the chromosome reference-based gene database build from 108 completely assembled L. monocytogenes reference genomesFile Phage_pangenome_reference.fa corresponds to the to the phage reference-based gene database build from 30 Listeria phage sequences obtained from NCBIFile Plasmids_pangenome_reference.fa corresponds to the plasmid reference-based gene database build from 41 Listeria plasmid sequences obtained from NCBI