Genetic diversity of dairy farm – associated Listeria monocytogenes

Authors: KIM, SEON-WOO - US Department Of Agriculture (USDA); HAENDIGES, JULIE - Maryland Department Of Health And Mental Hygiene; KELLER, ERIC - Maryland Department Of Health And Mental Hygiene; MYERS, ROBERT - Maryland Department Of Health And Mental Hygiene; KIM, ALEXANDER - Maryland Department Of Health And Mental Hygiene; LOMBARD, JASON - Animal And Plant Health Inspection Service (APHIS); KARNS, JEFFERY - US Department Of Agriculture (USDA); Van Kessel, Jo Ann; Haley, Bradd

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/25/2018
Publication Date: 5/9/2018
Citation: Kim, S., Haendiges, J., Keller, E.N., Myers, R., Kim, A., Lombard, J.E., Karns, J.S., Van Kessel, J.S., Haley, B.J. 2018. Genetic diversity of dairy farm – associated Listeria monocytogenes. PLoS One. 13(5):e0197053. https://doi.org/10.1371/journal.pone.0197053.
DOI: https://doi.org/10.1371/journal.pone.0197053

Interpretive Summary: Listeria monocytogenes is an environmentally-adapted foodborne pathogen that occasionally causes disease in humans and other mammals. It is the primary causative agent of listeriosis, manifestations of which can range from mild illness such as gastroenteritis in healthy individuals to severe infections of the central nervous system in immunocompromised, elderly, and young individuals. Although listeriosis is relatively uncommon, the fatality rate is high. Pregnant women are more likely to develop listeriosis than the general population and the result of this infection is often fatal for the fetus. Nonpasteurized dairy products are known to occasionally harbor Listeria monocytogenes and have been implicated in recent listeriosis outbreaks and numerous sporadic cases of listeriosis. However, the diversity of L. monocytogenes isolates recovered from these environments has not been adequately described. Understanding the diversity may provide information that helps us to more clearly understand the ecology of this organism and how that might human exposure. We sequenced the genomes of 129 L. monocytogenes isolates recovered from raw bulk tank dairy cow milk and environmental dairy farm samples from 19 states at three intervals over 12 years. We analyzed the sequenced genomes of the individual strains and compared them with each other. In an analysis of six locations on the genome (MVLST analysis), 62 different types (Virulence Types) were identified, of which 24% were Epidemic Clones that had previously been seen in other studies and 35 were novel, never seen before, virulence types. When seven genome locations were compared, 63 Sequence Types (ST) of 58 Clonal Complexes (CC) were identified. Multiple CCs previously associated with central nervous system and maternal-neonatal infections were identified. There was variable distribution of 80 virulence factors, portions of the genome that are known to impact how the bacteria colonize and invade the host. Some virulence factors were determined to be more frequently present in one bacterial lineage than the other. Results of this analysis indicate there is a high level of genetic diversity among L. monocytogenes present on dairy farms across the United States with some strains more frequently detected than others.

Technical Abstract: Nonpasteurized dairy products are known to occasionally harbor Listeria monocytogenes and have been implicated in recent listeriosis outbreaks and numerous sporadic cases of listeriosis. However, the diversity of L. monocytogenes isolates recovered from these environments has not been adequately described past the serogroup level and thus the true diversity of these isolates remains unknown. Here we report a genomic analysis of 129 L. monocytogenes isolates recovered from raw bulk tank dairy cow milk and environmental dairy farm samples from 19 states at three intervals over 12 years. In a six gene MVLST analysis, 62 Virulence Types (VT) were identified, of which 24% were Epidemic Clones I, II, V, VI, VII, VIII, X, or XI, and 35 were novel VT. In a seven gene MLST analysis, 63 Sequence Types (ST) of 58 Clonal Complexes (CC) were identified with the most common being CC7 (10% of isolates), CC37 (6%), CC29 (4.5%), and CC5 (4.5%). Multiple CCs previously associated with central nervous system and maternal-neonatal infections were identified. A genomic analysis identified variable distribution of 80 virulence factors, Listeria pathogenicity islands (LIPI) -1, -3, and -4, and stress survival island-1 (SSI-1). Of these, 19 virulence factors, including LIPI-3 and -4 were determined to be more frequently present in one lineage (I or II) than the other (Fisher’s Exact Test, P < 0.05). The pathogenicity island known to confer tropism for the placenta, LIPI-4, was identified in 16% of isolates. The prevalence of acquired genes conferring antibiotic resistance was low and consisted of tetR (tetracycline resistance) and ermB (erythromycin resistance). Results of this analysis indicate there is a high level of genetic diversity among L. monocytogenes present on dairy farms across the United States with some strains more frequently detected than others.