Microbial composition and dynamics in environmental samples from a ready-to-eat food production facility with a long-term colonisation of Listeria monocytogenes

doi:10.21203/rs.3.rs-3910281/v1

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Microbial composition and dynamics in environmental samples from a ready-to-eat food production facility with a long-term colonisation of Listeria monocytogenes

https://doi.org/10.21203/rs.3.rs-3910281/v1

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Background: Listeria monocytogenes is a foodborne pathogen of significant concern for the food industry due to the potential health threat to consumers and a remarkable ability to persist through food safety control efforts. Even with rigorous cleaning and disinfection practices in food production settings, L. monocytogenes and resident microbes can thrive and then potentially spillover from the environment to foods. Understanding the composition and interactions within microbial communities in food processing environments can reveal mechanisms on L. monocytogenes survival and persistence in these settings. In this study, we used metagenomic analysis to monitor the resident microbiota in non-food contact surfaces located in the preparation and production areas of the high care zone of a facility producing ready-to-eat foods that was previously known to have a persistent ST121 strain of L. monocytogenes.

Results: A consistent composition and relative abundance of most microbial taxa over sampling sites and times were observed in environmental metagenomes, with the genus Pseudomonas (principally Pseudomonas fluorescens) representing a major constituent of the metagenome. While there were highly related populations between the production and preparation areas, individual taxa characteristic of each area were observed (e.g., Sphingomonas aerolata was more abundant in the production area). Notably Listeria spp. were not observed in the metagenomes, but were detected in cultured samples, suggesting the abundance of Listeria was below the detection threshold for direct metagenomics. As such, a quasimetagenomics approach (sequencing of microbiological culture enrichments) was used to detect and subtype Listeria spp. and L. monocytogenes. While possible to classify Listeria seeligeri sequence types using quasimetagenomes, the classification of the L. monocytogenes sequence types was limited to a low proportion of the samples.

Conclusions: A stable resident microbiota was observed with multiple environmental-associated microbial taxa, emphasizing that non-contact food surfaces represent a niche that can be colonised by a community of interdependent microbes. This community was likely selected for by their collective ability to survive cleaning and disinfection control efforts in this environment. Listeria spp. was a member of this microbial community, albeit at very low abundance, and likewise may be benefiting from the mutualism of the overall microbial community.

Listeria monocytogenes

food processing environments

microbial ecology

metagenomics

No competing interests reported.

SupFig1.pdf
Supplementary Figure 1. Simplified map of the RTE-manufacturing facility. Sites A-I correspond to floor surfaces while site J corresponds to a drain. Preparation area is maintained at 4 °C while production area is maintained at 10 °C.
SupFig2.pdf
upplementary Figure 2. Log fold changes (LFC) of bias-corrected relative abundance at species level comparing the abundance at: A) production area against the preparation area and sampling times T2, T3 and T4 against T1. Negative fold changes (blue) represent lower bias-corrected abundances in the production area, T2 and T3 vs their respective comparator. Positive fold changes (red) represent lower bias-corrected abundances in the preparation area, T2 and T3 vs their respective comparator. B) production area against the preparation area and sampling times T1, T3 and T4 against T2. Negative fold changes (blue) represent lower bias-corrected abundances in the roduction area, T2 and T3 vs their respective comparator. Positive fold changes (red) represent lower bias-corrected abundances in the preparation area, T2 and T3 vs their respective comparator.
SupFig3.pdf
Supplementary Figure 3. Correlation analysis between species identified in the environmental samples. Colour scale represents the range of Spearman's rank correlation coefficient. Circles indicate statistical significance.
SupFig4.pdf
Supplementary Figure 4. Changes in bacterial diversity in environmental samples positive and negative for Listeria. A) Principal Coordinate Analysis of the Bray-Curtis distance level. The ellipses represent normal data ellipses for Listeria positive and negative samples. B) Alpha diversity evaluated with richness, Shannon and Simpson indexes depending on Listeria detection. Each boxplot represents the interquartile range (IQR) of the alpha diversity indexes values and the whiskers represent the minimum and maximum values. Statistical comparisons with the A) Adonis B) Wilcoxon tests are presented in supplementary materials. Only significant differences (p-value < 0.05) are indicated in the graphs.
SupFig5.pdf
Supplementary Figure 5. Microbial dynamics of Listeria enrichments in samples positive for L. seeligeri and negative for L. monocytogenes. Barplots show the relative abundance of A) the 10 most abundant genera and B) the 10 most abundant Listeria species identified in the enrichment using Illumina sequencing. The tables in panels B show the total number of reads produced on each sequencing library and the ST identified from the raw reads.
Supplementary.xlsx
Supplementary data Supplementary.xlsx

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Microbial composition and dynamics in environmental samples from a ready-to-eat food production facility with a long-term colonisation of Listeria monocytogenes

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