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ABSTRACT: Sequencing Listeria monocytogenes from retail delis

PROVIDER: PRJNA726543 | ENA |

REPOSITORIES: ENA

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			Action	DRS
		Other
	SRR14370000_1.fastq.gz	Fastqsanger.gz
	SRR14370000_2.fastq.gz	Fastqsanger.gz
	SRR14370001_1.fastq.gz	Fastqsanger.gz
	SRR14370001_2.fastq.gz	Fastqsanger.gz

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Transcriptomic analysis of biofilm formation in persistent and transient Listeria monocytogenes from the retail deli environment

Project description:Persistence of Listeria monocytogenes in retail deli environments is a serious food safety issue, potentially leading to cross-contamination of ready-to-eat foods such as deli meats, salads, and cheeses. We previously discovered strong evidence of L. monocytogenes persistence in delis across multiple states. We hypothesized that this was correlated with isolates’ innate characteristics, such as biofilm-forming capacity or gene differences.We further chose four isolates for RNA-sequencing analysis and compared their global biofilm transcriptome to their global planktonic transcriptome. Analysis of biofilm vs planktonic gene expression did not show the expected differences in gene expression patterns. Overall, L. monocytogenes persistence in the deli environment is likely a matter of poor sanitation and/or facility design, rather than isolates’ biofilm-forming capacity, sanitizer tolerance, or genomic content

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Project description:Listeria monocytogenes is a human, food-borne pathogen. Genomic comparisons between L. monocytogenes and Listeria innocua, a closely related non-pathogenic species, were pivotal in the identification of protein coding genes essential for virulence. However, no comprehensive comparison has focused on the non-coding genome. We used strand-specific cDNA sequencing to produce genome-wide transcription start site (TSS) maps for both organisms, and developed a publicly available integrative browser to visualize and analyze both transcriptomes in different growth conditions and genetic backgrounds. Our data revealed conservation across most transcripts, but significant divergence between the species in a subset of non-coding RNAs. In L. monocytogenes we identified 113 sRNAs and 70 asRNAs, significantly increasing the repertoire of non coding RNAs in this species. Remarkably, we identified a class of long antisense transcripts (lasRNAs) that overlap one gene while also serving as the 5M-bM-^@M-^Y UTR of the adjacent divergent gene. Experimental evidence suggests that lasRNAs transcription inhibits expression of one operon while activating the expression of another. Such lasRNA/operon structure, termed "excludon", might represent a novel form of regulation in bacteria. Construction of consensus TSS-maps in Listeria monocytogenes and Listeria innocua by applying 5'-end sequencing on samples in different conditions and genetic backgrounds.

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