Plasmidome of Listeria spp.—The repA-Family Business

Abstract

Bacteria of the genus Listeria (phylum Firmicutes) include both human and animal pathogens, as well as saprophytic strains. A common component of Listeria spp. genomes are plasmids, i.e., extrachromosomal replicons that contribute to gene flux in bacteria. This study provides an in-depth insight into the structure, diversity and evolution of plasmids occurring in Listeria strains inhabiting various environments under different anthropogenic pressures. Apart from the components of the conserved plasmid backbone (providing replication, stable maintenance and conjugational transfer functions), these replicons contain numerous adaptive genes possibly involved in: (i) resistance to antibiotics, heavy metals, metalloids and sanitizers, and (ii) responses to heat, oxidative, acid and high salinity stressors. Their genomes are also enriched by numerous transposable elements, which have influenced the plasmid architecture. The plasmidome of Listeria is dominated by a group of related replicons encoding the RepA replication initiation protein. Detailed comparative analyses provide valuable data on the level of conservation of these replicons and their role in shaping the structure of the Listeria pangenome, as well as their relationship to plasmids of other genera of Firmicutes, which demonstrates the range and direction of flow of genetic information in this important group of bacteria.

PervasiveListeria monocytogenesare common in the Norwegian food system and associated with increased prevalence of stress survival and resistance determinants

“…Overall, plasmids were identified in 58% of the L. monocytogenes isolates. All were repA -family theta-replicating plasmids belonging to either group 1 (G1) or group 2 (G2) (58), with one exception. Isolate MF6196 belonging to CC7 harbored a novel RepA group protein, hereby named RepA group 12 (G12), which was 76% identical to RepA G2 (Table 2).…”

“…The selection of plasmids included in the current analysis was based on a study by Chmielowska et al . (58), which included 113 unique completely sequenced plasmid replicons from Listeria spp. strains, of which 63 were assigned to 19 groups (different only by point mutations or small indels of size <1 kb).…”

“…A BLAST search for plasmid replication genes was carried out using one repA gene selected from each of the eleven RepA groups (G1-G11) identified by Chmielowska et al (58) as queries (Table S9), against a local nucleotide BLAST database created for the L. monocytogenes genomes. The same analysis was also performed using as queries the nine plasmid-encoded/associated genetic elements involved in stress response identified by Schmitz-Esser et al (63), as well as additional genetic elements associated with stress response and resistance (Table S4) and the entire content of the ResFinder database (59) downloaded on November 11, 2021.…”

Genomic characteristics of listeria that caused invasive listeriosis during the COVID-19 pandemic

“…The comparison of pLm with the Listeria plasmids deposited in GenBank showed high similarity to the pLIS19 (MZ089999), pLIS38 (MZ127847), and pLIS43 (MZ147615) plasmids of L. innocua strains, isolated from food and city environments in 2003-2017 in Poland [54] (Table 4). The ANI and AP among these plasmids are more than 99%.…”

“…. According to this classi cation, all of the analyzed plasmids belong to the repA_G1-Replication system group, which is the most common group [54]. All of the analyzed plasmids also carried two loci involved in the active partitioning of plasmid molecules (PAR_1 and additional parA), and the loci coding Y-family polymerase components (UvrX and YolD) representing the POL_1 group.…”