Hotspot mutations and ColE1 plasmids contribute to the fitness of Salmonella Heidelberg in poultry litter

Authors: OLADEINDE, ADELUMOLA - Orise Fellow; Cook, Kimberly - Kim; ORLEK, ALEX - University Of Oxford; Zock, Gregory; HERRINGTON, KYLER - University Of Georgia; Plumblee Lawrence, Jodie; Hall, Mary; Cox Jr, Nelson

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/31/2018
Publication Date: 8/31/2018
Citation: Oladeinde, A., Cook, K.L., Orlek, A., Zock, G.S., Herrington, K., Plumblee Lawrence, J.R., Hall, M.C., Cox Jr, N.A. 2018. Hotspot mutations and ColE1 plasmids contribute to the fitness of Salmonella Heidelberg in poultry litter. PLoS One. https://doi.org/10.1371/journal.pone.0202286.
DOI: https://doi.org/10.1371/journal.pone.0202286

Interpretive Summary: Salmonella enterica subsp. enterica serovar Heidelberg (S. Heidelberg) is a clinically-important serovar linked to food-borne illness, and commonly isolated from poultry. Investigations of a large, multistate outbreak in the USA in 2013 identified poultry litter as an important extra-intestinal environment that may have selected for specific S. Heidelberg strains. Poultry litter (PL) is a mixture of bedding materials and chicken excreta that contain chicken GI bacteria, undigested feed, feathers, and other materials of host origin. In this study, we performed a series of controlled laboratory experiments which assessed the evolution of two S. Heidelberg strains in PL previously used to raise 3 flocks of broiler chickens. Analysis of sequences with isolates recovered from poultry litter suggest that Col plasmids were taken up by S. Heidelberg from litter microbiota. Data from competition studies suggests that the Col plasmids contributed to persistence and did not impose a fitness cost on strains of S. Heidelberg from the poultry litter. Additionally, we observed a decrease in susceptibility to several antibiotics in Col plasmid-bearing strains. Our study demonstrates how acquisition of multiple Col-like plasmids can change the evolutionary path of S. Heidelberg in poultry litter.

Technical Abstract: Salmonella enterica subsp. enterica serovar Heidelberg (S. Heidelberg) is a clinically-important serovar linked to food-borne illness, and commonly isolated from poultry. Investigations of a large, multistate outbreak in the USA in 2013 identified poultry litter as an important extra-intestinal environment that may have selected for specific S. Heidelberg strains. Poultry litter (PL) is a mixture of bedding materials and chicken excreta that contain chicken GI bacteria, undigested feed, feathers, and other materials of host origin. In this study, we performed a series of controlled laboratory experiments which assessed the evolution of two S. Heidelberg strains (SH-2813 and SH-116) in PL previously used to raise 3 flocks of broiler chickens. The strains are closely related at the chromosome level, differing by only 69 single-nucleotide variants. Whole genome sequencing was performed on 86 isolates recovered after 0, 1, 7 and 14 days of evolution in PL. Only strains carrying an IncX1 (37kb), 2 ColE1 (4 and 6kb) and 1 ColpVC (2kb) plasmids survived more than 7 days in PL. Competition experiments showed that acquisition of these plasmids did not impose a fitness cost on evolved strains but instead increased their fitness. This increased fitness was associated with an increased copy number of IncX1 and ColE1 plasmids. Further, all Col plasmid-bearing strains had similar mutations in 102 genes encoded on the chromosome and in 3 genes encoded on the IncX1 plasmid Additionally, we observed a decrease in susceptibility to tobramycin, kanamycin, gentamicin, neomycin and fosfomycin for Col plasmid-bearing strains. Our study demonstrates how acquisition of multiple Col-like plasmids can change the evolutionary path of S. Heidelberg in poultry litter.