Determination of evolutionary relationships of outbreak-associated Listeria monocytogenes strains of serotypes 1/2a and 1/2b by whole-genome sequencing

Authors: BERGHOLZ, TERESA - North Dakota State University; DEN BAKKER, HENK - Cornell University; KATZ, LEE - Centers For Disease Control And Prevention (CDC) - United States; SILK, BENJAMIN - Centers For Disease Control And Prevention (CDC) - United States; JACKSON, KELLY - Centers For Disease Control And Prevention (CDC) - United States; KUCEROVA, ZUZANA - Centers For Disease Control And Prevention (CDC) - United States; JOSEPH, LAVIN - Centers For Disease Control And Prevention (CDC) - United States; TURNSEK, MARYANN - Centers For Disease Control And Prevention (CDC) - United States; GLADNEY, LORI - Centers For Disease Control And Prevention (CDC) - United States; HALPIN, JESSICA - Centers For Disease Control And Prevention (CDC) - United States; Ward, Todd; FRACE, MIKE - Centers For Disease Control And Prevention (CDC) - United States; TARR, CHERYL - Centers For Disease Control And Prevention (CDC) - United States

Submitted to: Applied and Environmental Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/18/2015
Publication Date: 2/1/2016
Publication URL: http://handle.nal.usda.gov/10113/62137
Citation: Bergholz, T.M., den Bakker, H.C., Katz, L.S., Silk, B.J., Jackson, K.A., Kucerova, Z., Joseph, L.A., Turnsek, M., Gladney, L.M., Halpin, J.L., Xavier, K., Gossack, J., Ward, T.J., Frace, M., Tarr, C.L. 2016. Determination of evolutionary relationships of outbreak-associated Listeria monocytogenes strains of serotypes 1/2a and 1/2b by whole-genome sequencing. Applied and Environmental Microbiology. 82(3):928-938.

Interpretive Summary: Listeria monocytogenes (Lm) is a food-borne bacterium that can cause serious illness in humans and other animals (listeriosis). Historically, strains of serotype 4b have caused most of the major listeriosis outbreaks. However in 2011, two other common serotypes, 1/2a and 1/2b were involved in one of the largest foodborne outbreaks in United States history. Isolates from this outbreak were genetically diverse and represented two previously unrecognized epidemic clone types. These results provided the impetus to use whole genome sequences to reconstruct the evolutionary relationships among Lm strains responsible for recent and historical outbreaks, as well as to place the strains into a clonal framework to better understand how outbreak strains are distributed within the diversity of Lm. Results of these analyses indicated that epidemic potential may be more widespread in Lm than previously understood. In addition, the results indicate that levels of genetic variation within individual epidemic clones can vary widely and may not be consistent with estimates of similarity derived from typing methods that are commonly employed in outbreak investigations. These findings highlight the need for increased sampling of isolates from patients and potential sources to ensure the entire diversity of strains involved in listeriosis outbreaks are identified, and will be of direct interest to epidemiologists, public health and food inspection agencies, and scientists involved in food safety research.

Technical Abstract: We used whole-genome sequencing to determine evolutionary relationships among 20 outbreak-associated clinical isolates of Listeria monocytogenes serotypes 1/2a and 1/2b. Isolates from 6 of 11 outbreaks fell outside the clonal groups or “epidemic clones” that have been previously associated with outbreaks, suggesting that epidemic potential may be widespread in L. monocytogenes and is not limited to the recognized epidemic clones. Pairwise comparisons between epidemiologically related isolates within clonal complexes showed that genome-level variation differed by 2 orders of magnitude between different comparisons, and the distribution of point mutations (core versus accessory genome) also varied. In addition, genetic divergence between one closely related pair of isolates from a single outbreak was driven primarily by changes in phage regions. The evolutionary analysis showed that the changes could be attributed to horizontal gene transfer; members of the diverse bacterial community found in the production facility could have served as the source of novel genetic material at some point in the production chain. The results raise the question of how to best utilize information contained within the accessory genome in outbreak investigations. The full magnitude and complexity of genetic changes revealed by genome sequencing could not be discerned from traditional subtyping methods, and the results demonstrate the challenges of interpreting genetic variation among isolates recovered from a single outbreak. Epidemiological information remains critical for proper interpretation of nucleotide and structural diversity among isolates recovered during outbreaks and will remain so until we understand more about how various population histories influence genetic variation.