comK Prophage Junction Fragments as Markers for Listeria monocytogenes Genotypes Unique to Individual Meat and Poultry Processing Plants and a Model for Rapid Niche-Specific Adaptation, Biofilm Formation, and Persistence

Abstract

Different strains of Listeria monocytogenes are well known to persist in individual food processing plants and to contaminate foods for many years; however, the specific genotypic and phenotypic mechanisms responsible for persistence of these unique strains remain largely unknown. Based on sequences in comK prophage junction fragments, different strains of epidemic clones (ECs), which included ECII, ECIII, and ECV, were identified and shown to be specific to individual meat and poultry processing plants. The comK prophage-containing strains showed significantly higher cell densities after incubation at 30°C for 48 h on meat and poultry food-conditioning films than did strains lacking the comK prophage (P < 0.05). Overall, the type of strain, the type of conditioning film, and the interaction between the two were all highly significant (P < 0.001). Recombination analysis indicated that the comK prophage junction fragments in these strains had evolved due to extensive recombination. Based on the results of the present study, we propose a novel model in which the concept of defective comK prophage was replaced with the rapid adaptation island (RAI). Genes within the RAI were recharacterized as "adaptons," as these genes may allow L. monocytogenes to rapidly adapt to different food processing facilities and foods. If confirmed, the model presented would help explain Listeria's rapid niche adaptation, biofilm formation, persistence, and subsequent transmission to foods. Also, comK prophage junction fragment sequences may permit accurate tracking of persistent strains back to and within individual food processing operations and thus allow the design of more effective intervention strategies to reduce contamination and enhance food safety.Listeria monocytogenes is a unique food-borne pathogen that causes listeriosis, which ranges from febrile gastroenteritis to more severe life-threatening invasive diseases, especially for immunocompromised individuals (94). It is widely distributed in many wild and domestic animals and various natural environments and is resistant to a wide variety of environmental stresses (33). L. monocytogenes is considered a model organism for the study of host-pathogen interactions, especially as a model for intracellular pathogens of humans (47). However, L. monocytogenes may also be an excellent model for pathogenenvironment interactions, because it is well known to cycle between being a pathogen in many wild and domestic animals and a saprophyte in diverse environments, including those found in various types of food processing facilities (41). However, while much is known about the pathogenic lifestyle of L. monocytogenes, much less is known about its saprophytic lifestyle, including the genetic and phenotypic factors affecting its colonization and persistence in food processing and retail environments and subsequent transmission to ready-to-eat (RTE) foods. This has resulted in numerous costly recalls, disease cases, and outbreaks, which are often associated with high mortality (94). As a res...

Genome Sequencing Identifies Two Nearly Unchanged Strains of Persistent Listeria monocytogenes Isolated at Two Different Fish Processing Plants Sampled 6 Years Apart

“…Alternatively, the results may represent a relic of a previous phage insertion and subsequent deletion event. If the two Listeria strains do contain a prophage in comK, it could potentially be involved in the persistence mechanism (39).…”

Comparative Genomics Reveals the Diversity of Restriction-Modification Systems and DNA Methylation Sites in Listeria monocytogenes

“…Neither clonal complex, time of isolation, nor serotype can be used as a predictive determinant of in vitro invasiveness even when isolates belong to the same serotype or clonal complex, confirming that previously assigned classification phenotypes are not predictors of invasiveness. As an organism under high purifying selection in systems of food production (47), L. monocytogenes relies on the presence of phage elements to introduce phenotypic variability, allowing for rapid adaptation to different environments (48). Genome sequencing and subsequent analyses revealed unexpected differences in genome structure and diverse and unique methyltransferase motifs and methylome patterns.…”

The Connection between Persistent, Disinfectant-Resistant Listeria monocytogenes Strains from Two Geographically Separate Iberian Pork Processing Plants: Evidence from Comparative Genome Analysis

“…The lack of an intact prophage insertion in comK has been reported for most of the ST121 strains (34). Strains without the insertion in comK, such as the strain of PFGE type S10-1, could evolve to contain a prophage in comK, and it could potentially be involved in the persistence mechanism (72).…”

“…Bacteriophages also play an important role in the acquisition of traits by L. monocytogenes that can increase survival capacity (63,64). For example, phages inserted into the comK gene might provide fitness advantages in food production environments (20), encoding, for example, the ability for rapid niche-specific adaptation, biofilm formation, and persistence (72). In this study, a prophage sequence was present as an insertion into comK in four strains, whereas it was absent in the strain of PFGE type S10-1 ( Table 4).…”