Prevalence and clonal diversity of over 1,200 Listeria monocytogenes isolates collected from public access waters near produce production areas on the central California coast during 2011 to 2016

Authors: Gorski, Lisa; Cooley, Michael; ORYANG, DAVID - Food And Drug Administration(FDA); Carychao, Diana; NGUYEN, KIMBERLY - Food Safety Inspection Service (FSIS); LUO, YAN - Food And Drug Administration(FDA); WEINSTEIN, LEAH - Food And Drug Administration(FDA); BROWN, ERIC - Food And Drug Administration(FDA); ALLARD, MARC - Food And Drug Administration(FDA); MANDRELL, ROBERT - Retired ARS Employee; CHEN, YI - Food And Drug Administration(FDA)

Submitted to: Applied and Environmental Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/1/2022
Publication Date: 4/26/2022
Citation: Gorski, L.A., Cooley, M.B., Oryang, D., Carychao, D.K., Nguyen, K., Luo, Y., Weinstein, L., Brown, E., Allard, M., Mandrell, R., Chen, Y. 2022. Prevalence and clonal diversity of over 1,200 Listeria monocytogenes isolates collected from public access waters near produce production areas on the central California coast during 2011 to 2016. Applied and Environmental Microbiology. 88(8). Article e00357.22. https://doi.org/10.1128/aem.00357-22.
DOI: https://doi.org/10.1128/aem.00357-22

Interpretive Summary: The foodborne pathogen Listeria monocytogenes lives in nature associated with decaying plant matter, water, and in wildlife. From this niche it can interact with and contaminate pre-harvest produce. Strains of L. monocytogenes from clinical and food processing plant sources are well documented, and the genomic subtypes of these strains is beginning to be understood. The genomic subtypes of environmental strains of L. monocytogenes is not well studied. Part of the reason for this knowledge gap is a lack of strains from environmental sources. A 5-year survey of public access surface waters in a large agricultural region of Central Coastal California was done to assess the prevalence of the foodborne pathogen, Listeria monocytogenes in nature. During 2011 – 2016, nearly 3,000 samples of water and sediment were collected from lakes, ponds, streams, and rivers, and enriched to detect L. monocytogenes. A total of 1, 224 samples tested positive, resulting in a 41.9% prevalence of the pathogen in the region. L. monocytogenes was more likely to be found during the winter and spring months, and after large rain events. Over 84% of the isolates obtained were of serotype 4b, which is a serotype often implicated in foodborne illness and outbreaks. Most of the strains were subjected to Whole Genome Sequencing, and the in silico Multi Locus Sequence Typing revealed 75 different genomic subtypes. All of the sequenced isolates contained the core virulence genes needed for L. monocytogenes to cause illness in people. Additional virulence genes responsible for more serious illness were detected in over 60% of the strains. One of the most common genomic subtypes was CC183, which is an emerging subtype responsible for three produce-related outbreaks in the last 7 years. Genes commonly found in food processing plant isolates of L. monocytogenes, such as those encoding resistance to sanitizers, were not well represented in this environmental collection. Results indicate a high diversity of L. monocytogenes strains that contain virulence genes.

Technical Abstract: A 5-year survey of public access surface waters in a large agricultural region of Central Coastal California was done to assess the prevalence of the foodborne pathogen, Listeria monocytogenes. In nature, L. monocytogenes lives as a saprophyte in soil and water, which are reservoirs for contamination of pre-harvest produce. Moore swabs were deployed biweekly in lakes, ponds, streams, and rivers during 2011 – 2016. L. monocytogenes was recovered in 1,224 of 2,922 samples, resulting in 41.9% prevalence. Multiple subtypes were isolated from 97 samples, resulting in 1,323 L. monocytogenes isolates. Prevalence was higher in winter and spring and after rain events. Over 84% of the isolates were serotype 4b. Whole genome sequencing was done on 1,248 isolates, and in silico Multi Locus Sequence Typing revealed 75 different Sequence Types (ST) and 40 Clonal Complexes (CC). The most isolated clonal types, CC639, CC183, and CC1, made up 27%, 19%, and 13%, respectively, of the sequenced isolates. Other types were CC663, CC6, CC842, CC4, CC2, CC5, and CC217. All sequenced isolates contained intact copies of core L. monocytogenes virulence genes, and pathogenicity islands LIPI-3 and LIPI-4 were identified in 73% and 63%, respectively, of the sequenced isolates. The virulence factor internalin A was predicted to be intact in all but four isolates, while genes important for sanitizer and heavy metal resistance were found in < 5% of the isolates. These waters are not used for crop irrigation directly, but they are available to wildlife and can flood fields during heavy rains.Listeria monocytogenes serotype 4b and 1/2a strains are implicated in most listeriosis illness, and hypervirulent listeriosis stems from strains containing pathogenicity islands LIPI-3 and LIPI-4. The waters and sediments in this agricultural region contain highly prevalent and diverse L. monocytogenes populations, and all the isolates contain intact virulence genes. Emerging clones CC183 and CC639 were the most abundant clonal types, and major clonal groups CC1, CC4, and CC6 were well represented. CC183 was responsible for three produce-related outbreaks in the last seven years. Most of the isolates in the survey differ from those of lesser virulence that are often isolated from foods and food processing plants because they contain genes encoding an intact virulence factor Internalin A, and most did not contain genes for sanitizer and heavy metal resistance. This isolate collection is important for understanding L. monocytogenes populations in agricultural and natural regions.