Mungo bean sprout microbiome and changes associated with culture based enrichment protocols used in detection of Gram-negative foodborne pathogens.

Heike Margot,Taurai Tasara,Roger Stephan

doi:10.1186/s40168-016-0193-y

Abstract

BackgroundFresh sprouted seeds have been associated with a number of large outbreaks caused by Salmonella and Shiga toxin-producing E. coli. However, the high number of commensal bacteria found on sprouted seeds hampers the detection of these pathogens. Knowledge about the composition of the sprout microbiome is limited. In this study, the microbiome of mungo bean sprouts and the impact of buffered peptone water (BPW) and Enterobacteriaceae enrichment broth (EE-broth)-based enrichment protocols on this microbiome were investigated.ResultsAssessments based on aerobic mesophilic colony counts showed similar increases in mungo bean sprout background flora levels independent of the enrichment protocol used. 16S rRNA sequencing revealed a mungo bean sprout microbiome dominated by Proteobacteria and Bacteroidetes. EE-broth enrichment of such samples preserved and increased Proteobacteria dominance while reducing Bacteroidetes and Firmicutes relative abundances. BPW enrichment, however, increased Firmicutes relative abundance while decreasing Proteobacteria and Bacteroidetes levels. Both enrichments also lead to various genus level changes within the Protobacteria and Firmicutes phyla.ConclusionsNew insights into the microbiome associated with mungo bean sprout and how it is influenced through BPW and EE-broth-based enrichment strategies used for detecting Gram-negative pathogens were generated. BPW enrichment leads to Firmicutes and Proteobacteria dominance, whereas EE-broth enrichment preserves Proteobacteria dominance in the mungo bean sprout samples. By increasing the relative abundance of Firmicutes, BPW also increases the abundance of Gram-positive organisms including some that might inhibit recovery of Gram-negative pathogens. The use of EE-broth, although preserving and increasing the dominance of Proteobacteria, can also hamper the detection of lowly abundant Gram-negative target pathogens due to outgrowth of such organisms by the highly abundant non-target Proteobacteria genera comprising the mungo bean sprout associated background flora.

Highlights

Fresh sprouted seeds have been associated with a number of large outbreaks caused by Salmonella and Shiga toxin-producing E. coli
Assessments based on aerobic mesophilic colony counts showed similar increases in mungo bean sprout background flora levels independent of the enrichment protocol used. 16S rRNA sequencing revealed a mungo bean sprout microbiome dominated by Proteobacteria and Bacteroidetes
buffered peptone water (BPW) enrichment, increased Firmicutes relative abundance while decreasing Proteobacteria and Bacteroidetes levels. Both enrichments lead to various genus level changes within the Protobacteria and Conclusions: New insights into the microbiome associated with mungo bean sprout and how it is influenced through BPW and EE-broth-based enrichment strategies used for detecting Gram-negative pathogens were generated

Summary

Introduction

Fresh sprouted seeds have been associated with a number of large outbreaks caused by Salmonella and Shiga toxin-producing E. coli. Aerobic bacterial counts as high as 107 to 109 cfu/g and the presence of foodborne pathogens such as Salmonella, Shigatoxinproducing Escherichia coli (STEC), and Listeria monocytogenes have been reported in alfalfa, fenguk, and mungo bean sprouts samples collected at retail level in different countries [2,3,4,5,6,7]. Sprouted seeds contaminated with enteric pathogens have been associated with many large illness outbreaks, most of which have been linked to Salmonella and STEC [3, 8, 9]. Newport infections occurred during 2011 in Germany and Netherlands following the consumption of contaminated mungo bean sprouts [8]. Enteritidis-contaminated mungo bean sprouts involved several states and caused cases of illness during 2014 in the USA [9]

Methods

Results

Conclusion