Comparative genomics and transcriptomics of lineages I, II, and III strains of Listeria monocytogenes

Abstract

BackgroundListeria monocytogenes is a food-borne pathogen that causes infections with a high-mortality rate and has served as an invaluable model for intracellular parasitism. Here, we report complete genome sequences for two L. monocytogenes strains belonging to serotype 4a (L99) and 4b (CLIP80459), and transcriptomes of representative strains from lineages I, II, and III, thereby permitting in-depth comparison of genome- and transcriptome -based data from three lineages of L. monocytogenes. Lineage III, represented by the 4a L99 genome is known to contain strains less virulent for humans.ResultsThe genome analysis of the weakly pathogenic L99 serotype 4a provides extensive evidence of virulence gene decay, including loss of several important surface proteins. The 4b CLIP80459 genome, unlike the previously sequenced 4b F2365 genome harbours an intact inlB invasion gene. These lineage I strains are characterized by the lack of prophage genes, as they share only a single prophage locus with other L. monocytogenes genomes 1/2a EGD-e and 4a L99. Comparative transcriptome analysis during intracellular growth uncovered adaptive expression level differences in lineages I, II and III of Listeria, notable amongst which was a strong intracellular induction of flagellar genes in strain 4a L99 compared to the other lineages. Furthermore, extensive differences between strains are manifest at levels of metabolic flux control and phosphorylated sugar uptake. Intriguingly, prophage gene expression was found to be a hallmark of intracellular gene expression. Deletion mutants in the single shared prophage locus of lineage II strain EGD-e 1/2a, the lma operon, revealed severe attenuation of virulence in a murine infection model.ConclusionComparative genomics and transcriptome analysis of L. monocytogenes strains from three lineages implicate prophage genes in intracellular adaptation and indicate that gene loss and decay may have led to the emergence of attenuated lineages.

Listeria monocytogenes Strains Underrepresented during Selective Enrichment with an ISO Method Might Dominate during Passage through Simulated Gastric Fluid and In Vitro Infection of Caco-2 Cells

“…As aforementioned, the production of monocins might confer a competitive advantage to the producing L. monocytogenes strains during selective enrichment. The monocin locus, a highly conserved cryptic prophage region that includes the lma operon, has been shown to play a role also in the intracellular growth of L. monocytogenes inside macrophages (56,57), and the presence of a complete lma operon in a L. monocytogenes strain has been suggested to be involved in the finding that its virulence was higher than that seen with a strain harboring a truncated lma operon (58). Nevertheless, besides the interstrain genomic differences which might explain strain advantages or disadvantages under certain environments, the stimuli and conditions that trigger the expression of factors related to enrichment or virulence competition are also unknown and may well be subject to strain variations.…”

The evolution and epidemiology of Listeria monocytogenes in Europe and the United States

“…For a number of microorganisms, studies have analyzed the core genome to specifically characterize the genus/species, and the accessory genome has been extensively analyzed with the aim to evaluate the evolution and adaptability of a particular genus/species (Deng et al, 2010;Gordienko et al, 2013;Leekitcharoenphon et al, 2012;Muzzi and Donati, 2011;Smokvina et al, 2013). A similar number of core genes in the L. monocytogenes genome was observed across different studies: 2032 genes (den Bakker et al, 2010), 2330-2456 (Deng et al, 2010), 2570-2725 (Hain et al, 2012), and 2354 (Kuenne et al, 2013). It has been estimated that a single strain of L. monocytogenes carries about 75% of the pan genes of the species and thus assays run on a limited number of reference strains may not reflect the total diversity of L. monocytogenes (Deng et al, 2010).…”

“…monocytogenes chromosomes were also found to include, at three different loci, parts of a defense immune system against bacteriophages, such as CRISPRs (i.e. clustered regularly interspaced short palindromic repeats) and associated genes (cas genes) (Hain et al, 2012;Kuenne et al, 2013). Hain and colleagues observed locus I to be highly conserved in the analyzed strains (two of serotype 4b, one 1/2a and a L. innocua one), while locus II was only found in three 4a strains, and absent in one other strain of lineage III (belonging to serotype 4c).…”

An Effective Counterselection System for Listeria monocytogenes and Its Use To Characterize the Monocin Genomic Region of Strain 10403S

“…Furthermore, temperature-dependent differential expression and secretion of the proteins encoded by these genes were demonstrated (30). In a much more recent work, published in 2012, Hain et al refer to the lma region in the EGD-e strain as a phage remnant and a monocin due to the fact that most of its open reading frames (ORFs) are related to phage genes, including a holin and endolysin module, while noticing that it lacks essential phage functions such as capsid structural genes (31). They show this region to be the only locus of phage origin conserved between Listeria lineages.…”