Large-scale Bioinformatic and Phylogenetic Analysis of Listeria monocytogenes Genomes Reveal Select InlA Genotypes Associated with Virulence and Transmission in Ecological Food Niches

Introduction: The foodborne pathogen, Listeria monocytogenes, exhibits fitness in diverse ecological niches, including mammalian hosts, agricultural, and food environments. Human listeriosis is predominantly associated with contaminated ready-to-eat (RTE) deli meats and cheese, however recent outbreaks associated with produce (e.g., sprouts) and fruit (e.g., caramel apples) indicate agricultural environments may serve as an emerging ecological niche for multiplication and transmission of pathogenic L. monocytogenes. Internalin A, is encoded by inlA and mediates host colonization. Several mutations leading to truncated InlA protein are associated with attenuated virulence phenotypes and are enriched among food isolates but rare among clinical isolates.

Purpose: Our study sought to analyze distinct InlA functional and genotypic variants associated with L. monocytogenes from food and clinical sources.

Methods: We utilized phylogenetic and bioinformatic methods to analyze distribution of distinct InlA functional and sequence variants identified among 2209 genomes representing isolates from various sources.

Results: InlA non-functional subtypes were significantly (P<0.001) associated with food categories (dairy, produce, and ready-to-eat (RTE)). Among lineage I and lineage II, respectively, functional InlA variants were significantly enriched among RTE isolates (17.7% and 43.8%; P<0.0001), while functional subtypes were enriched among produce (99.1% and 91.3%; P<0.0001) isolates. We further analyzed the distribution of InlA PST subtypes within L. monocytogenes. Overall, 252 unique InlA PST were identified among strains from lineage I (n=45) and lineage II (n = 113). Individual InlA PST variants were distinct for each lineage and isolate source for lineage I strains. Four InlA PST were enriched among lineage I strains from clinical (77.8%), food (44.5%) and environmental (34.2%) sources; these InlA variants also represented the most frequent subtype present among all produce and dairy isolates.

Significance: Our results indicate inlA genetic variation may contribute to distinct ecological preference and multiplication and transmission of pathogenic L. monocytogenes via host-dependent dispersal mechanisms in agricultural environments.