Enrichment dynamics of Listeria monocytogenes and the associated microbiome from naturally contaminated ice cream linked to a listeriosis outbreak

BMC Microbiology

Research Article

Poorani Subramanian¹  Nur Hasan¹  Rita Colwell¹  Christopher Grim²  Ninalynn Daquiqan²  Darcy Hanes²  Karen Jarvis²  Padmini Ramachandran³  Eric Brown³  Andrea Ottesen³  Gina Ryan³  Elizabeth Reed³  Yi Chen³  Marc Allard³  James R. White⁴ 

[1] CosmosID, 155 Gibbs Street, 20850, Rockville, MD, USA;Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, Food and Drug Administration, 8301 Muirkirk Road, 20708, Laurel, MD, USA;Office of Regulatory Science, Center for Food Safety and Applied Nutrition, Food and Drug Administration, 5001 Campus Drive, 20740, College Park, MD, USA;Resphera Biosciences, 1529 Lancaster Street, 21231, Baltimore, MD, USA;

关键词: Listeria monocytogenes;    Enrichment;    Ice cream;    Microbiota;    Co-enriching bacteria;    16S rRNA;    Shotgun metagenomics;    Next-generation sequencing;    NGS;    ISO;    FDA;    USDA;    Listeria;    Half-Fraser broth (HFB);    Fraser broth (FB);    University of Vermont modified broth (UVM);   

DOI  :  10.1186/s12866-016-0894-1

 received in 2016-09-11, accepted in 2016-11-11,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundMicrobiota that co-enrich during efforts to recover pathogens from foodborne outbreaks interfere with efficient detection and recovery. Here, dynamics of co-enriching microbiota during recovery of Listeria monocytogenes from naturally contaminated ice cream samples linked to an outbreak are described for three different initial enrichment formulations used by the Food and Drug Administration (FDA), the International Organization of Standardization (ISO), and the United States Department of Agriculture (USDA). Enrichment cultures were analyzed using DNA extraction and sequencing from samples taken every 4 h throughout 48 h of enrichment. Resphera Insight and CosmosID analysis tools were employed for high-resolution profiling of 16S rRNA amplicons and whole genome shotgun data, respectively.ResultsDuring enrichment, other bacterial taxa were identified, including Anoxybacillus, Geobacillus, Serratia, Pseudomonas, Erwinia, and Streptococcus spp. Surprisingly, incidence of L. monocytogenes was proportionally greater at hour 0 than when tested 4, 8, and 12 h later with all three enrichment schemes. The corresponding increase in Anoxybacillus and Geobacillus spp.indicated these taxa co-enriched in competition with L. monocytogenes during early enrichment hours. L. monocytogenes became dominant after 24 h in all three enrichments. DNA sequences obtained from shotgun metagenomic data of Listeria monocytogenes at 48 h were assembled to produce a consensus draft genome which appeared to have a similar tracking utility to pure culture isolates of L. monocytogenes.ConclusionsAll three methods performed equally well for enrichment of Listeria monocytogenes. The observation of potential competitive exclusion of L. mono by Anoxybacillus and Geobacillus in early enrichment hours provided novel information that may be used to further optimize enrichment formulations. Application of Resphera Insight for high-resolution analysis of 16S amplicon sequences accurately identified L. monocytogenes. Both shotgun and 16S rRNA data supported the presence of three slightly variable genomes of L. monocytogenes. Moreover, the draft assembly of a consensus genome of L. monocytogenes from shotgun metagenomic data demonstrated the potential utility of this approach to expedite trace-back of outbreak-associated strains, although further validation will be needed to confirm this utility.

【 授权许可】

CC BY   
© The Author(s). 2016