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Title: Listeria monocytogenes from food processing plants : Longitudinal sampling of Listeria monocytogenes from food processing plants reveals genomic diversity and dates the emergence of persisting sequence types of this food-borne pathogen      
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ID:
PRJEB14063
description:
Listeriosis is caused by the foodborne pathogen Listeria monocytogenes and contamination of food from bacteria persisting in the production environment is often the source. Whole genome sequencing (WGS) is increasingly used for tracing sources of outbreaks and addressing the molecular basis of persistence; however, this requires understanding of the inter- and intra-plant genomic diversity. Based on WGS of a collection of 90 L. monocytogenes strains isolated from food processing plants over 20 years (1995-2004 and 2013-2014), we found a high genomic stability of L. monocytogenes, enabling a detailed analysis of individual sequence types as defined by multi locus sequence typing (MLST). Across multiple sites and years, we identified three persistent sequence types ST7, ST8 and ST121 that are all were estimated to have emerged ~100 years ago, which correlates with the onset of industrialization and globalization of the food market. Mutation rates of these persisting sequence types were estimated to be 0.18, 0.30, and 0.35 SNP/year, respectively, which are among the lowest reported for bacterial pathogens. Clonality of the persisting and non-persisting isolates was investigated, and several sequence types had clonal groups of isolates with ≤4 SNPs including ST7 and ST121, but the number of long-term persisting clonal groups was limited, and new clones were introduced continuously, potentially from raw materials. Genes previously assumed to be involved in persistence were distributed in a sequence type dependent manner, and no common pattern could explain persistence. Nonetheless, the accessory genome for ST7, ST8 and ST121 encoded genes involved in resistance towards phages and biocides that could enhance persistence in the processing environment. Overall, our genomic analysis of a longitudinal and diverse collection of L. monocytogenes isolates provide insight into inter- and intra-plant genomic diversity that together with estimates of L. monocytogenes mutation rates in a natural environment help to track and establish the emergence of persistent sequence types.
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landingpage: http://www.ncbi.nlm.nih.gov/bioproject/PRJEB14063
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abbreviation:
NCBI
homePage: http://www.ncbi.nlm.nih.gov
ID:
SCR:006472
name:
National Center for Biotechnology Information
homePage: http://www.ncbi.nlm.nih.gov/bioproject
ID:
SCR:004801
name:
NCBI BioProject