Genetic diversity and virulence gene profiles of Listeria monocytogenes isolates from the 2010-2013 interagency market basket survey

Authors: CHEN, YI - Food And Drug Administration(FDA); CHEN, YUHUAN - Food And Drug Administration(FDA); POUILLOT, REGIS - Consultant; DENNIS, SHERRI - Food And Drug Administration(FDA); XIAN, ZHIHAN - Food And Drug Administration(FDA); Luchansky, John; Porto-Fett, Anna; Lindsay, James; ALLARD, MARK - Food And Drug Administration(FDA); BROWN, ERIC - Food And Drug Administration(FDA); VAN DOREN, JANE - Food And Drug Administration(FDA)

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/24/2020
Publication Date: 3/24/2020
Citation: Chen, Y., Chen, Y., Pouillot, R., Dennis, S., Xian, Z., Luchansky, J.B., Porto Fett, A.C., Lindsay, J.A., Allard, M., Brown, E., Van Doren, J.M. 2020. Genetic diversity and virulence gene profiles of Listeria monocytogenes isolates from the 2010-2013 interagency market basket survey. PLoS One. https://doi.org/10.1371/journal.pone.0231393.
DOI: https://doi.org/10.1371/journal.pone.0231393

Interpretive Summary: Listeria monocytogenes has been responsible for appreciable human illness and numerous recalls of ready-to-eat (RTE) food products. Between 2010 and 2013, a collection of 201 isolates of L. monocytogenes were recovered from 102 of 27,389 (RTE) foods purchased at grocery stores in the U.S. as part of the Interagency Market Basket Survey (Lm MBS).To better understand the genetic diversity of these isolates, we performed whole genome sequencing (WGS) analyses of the L. monocytogenes isolates that were recovered from selected RTE food groups, such as produce, seafood, dairy, meat, eggs, and combination foods such as sandwiches. In addition, analyses were conducted to determine presence/absence of major virulence genes and genes implicated in persistence of the pathogen in foods. Results demonstrated the presence of 29 clones among the 201 isolates. No significant differences in genetic diversity were found following pairwise comparisons of isolates; however, the full-length virulence gene inlA was present in 89.4% of the isolates. The identification of multiple clusters of isolates, along with well-documented metadata, may be used to assess and manage risks from L. monocytogenes associated with the consumption of RTE foods. Overall, this study generated unique insights into clonal groups and virulence gene profiles in a well-defined set of 201 isolates recovered from selected categories of refrigerated, RTE foods purchased at retail in the U.S. over a 3-year period.

Technical Abstract: Whole genome sequencing (WGS) was performed on 201 isolates of Listeria monocytogenes recovered from 102 of 27,389 ready-to-eat (RTE) foods purchased at grocery stores within four FoodNet sites in the U.S. between 2010-2013 as part of the Interagency Market Basket Survey (Lm MBS). Core genome multi-locus sequence typing (cgMLST) and in-silico analyses were conducted and compared with metadata for these 201 isolates obtained from among the following six Lm MBS food groups tested: produce, seafood, dairy, meat, eggs, and combination foods such as sandwiches. Two isolates were retained from each of 99 food samples, but only a single isolate was retained from the remaining 3 other food (sprout) samples. For 91 of 96 food samples tested, both isolates from the same sample were shown to be indistinguishable by WGS. The sequence type and clonal complex (CC), along with major virulence genes and genes implicated in persistence, such as Listeria Pathogenicity Islands 1, 3, and 4, internalins (inlABEFGHJK), Sigma factor B, and Stress Survival Islets 1 and 2, were determined for each isolate. Results revealed that among the 29 clones identified, the five most prevalent were CC155, CC1, CC5, CC87 and CC321. The Shannon’s diversity index for clones per food group ranged from 1.49 for dairy to 2.32 for produce, but no significant differences in diversity were found following pairwise comparisons of isolates. The most common serogroups were 1/2a and 3a (45.2%), followed by 1/2b and 3b (26.9%), 4b, 4d and 4e (20.2%), and 1/2c and 3c (4.8%). The proportions of isolates within Lineages I, II, and III were 48.1%, 50.0%, and 1.9%, respectively. Full-length inlA was present in 89.4% of the isolates without a premature stop codon (PMSC). These findings demonstrated a significant shift towards a higher percentage of Lineage I isolates and isolates not-containing inlA PMSCs when compared with a previous study conducted over a decade ago. Overall, this study generated unique insights into clonal groups and virulence gene profiles in a well-defined set of 201 isolates recovered from selected categories of refrigerated, RTE foods purchased at retail in the U.S. over a 3-year period.