Enrichment dynamics of Listeria monocytogenes and the associated microbiome from naturally contaminated ice cream linked to a listeriosis outbreak
| Autor: | Christopher J. Grim, Padmini Ramachandran, Poorani Subramanian, Marc W. Allard, Nur A. Hasan, Yi Chen, Karen G. Jarvis, James R. White, Elizabeth Reed, Eric W. Brown, Gina Ryan, Andrea Ottesen, Ninalynn Daquiqan, Darcy E. Hanes, Rita R. Colwell |
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| Rok vydání: | 2016 |
| Předmět: |
Ice cream
DNA Bacterial 0301 basic medicine Microbiology (medical) Shotgun metagenomics 030106 microbiology Anoxybacillus Co-enriching bacteria Biology medicine.disease_cause Microbiology Geobacillus University of Vermont modified broth (UVM) Disease Outbreaks Foodborne Diseases 03 medical and health sciences Buffered Listeria enrichment broth (BLEB) Listeria monocytogenes medicine ISO Humans Food microbiology Listeriosis 16S rRNA United States Department of Agriculture USDA Bacteriological Techniques United States Food and Drug Administration Shotgun sequencing Microbiota Fraser broth (FB) Half-Fraser broth (HFB) 16S ribosomal RNA DNA extraction United States 030104 developmental biology Enrichment Metagenomics NGS Next-generation sequencing Food Microbiology FDA Research Article |
| Zdroj: | BMC Microbiology |
| ISSN: | 1471-2180 |
| DOI: | 10.1186/s12866-016-0894-1 |
| Popis: | Background Microbiota 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. Results During 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. Conclusions All 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. Electronic supplementary material The online version of this article (doi:10.1186/s12866-016-0894-1) contains supplementary material, which is available to authorized users. |
| Databáze: | OpenAIRE |
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