Hiding in Fresh Fruits and Vegetables: Opportunistic Pathogens May Cross Geographical Barriers

Abstract

Different microbial groups of the microbiome of fresh produce can have diverse effects on human health. This study was aimed at identifying some microbial communities of fresh produce by analyzing 105 samples of imported fresh fruits and vegetables originated from different countries in the world including local samples (Oman) for aerobic plate count and the counts of Enterobacteriaceae, Enterococcus, and Staphylococcus aureus. The isolated bacteria were identified by molecular (PCR) and biochemical methods (VITEK 2). Enterobacteriaceae occurred in 60% of fruits and 91% of vegetables. Enterococcus was isolated from 20% of fruits and 42% of vegetables. E. coli and S. aureus were isolated from 22% and 7% of vegetables, respectively. Ninety-seven bacteria comprising 21 species were similarly identified by VITEK 2 and PCR to species level. E. coli, Klebsiella pneumoniae, Enterococcus casseliflavus, and Enterobacter cloacae were the most abundant species; many are known as opportunistic pathogens which may raise concern to improve the microbial quality of fresh produce. Phylogenetic trees showed no relationship between clustering of the isolates based on the 16S rRNA gene and the original countries of fresh produce. Intercountry passage of opportunistic pathogens in fresh produce cannot be ruled out, which requires better management.

Figure 1

Microbial counts (log (mean + 1) CFU g⁻¹) in local fruits (LF), imported fruits (IF), local vegetables (LV), and imported vegetables (IV).

Figure 2

Neighbor joining tree based on 16S rRNA gene sequences of members of Enterobacteriaceae isolated from fresh produce. Staphylococcus aureus (JN102565) was included as an outgroup. KR-accession numbers correspond to gene sequences that belong to isolates analyzed in this study while others were obtained from NCBI database. Bootstrap values above 50% are shown (1000 replications).

Figure 3

Neighbor joining tree based on 16S rRNA gene sequences of E. coli isolated from fresh produce. E. coli strain JCM 24006 (AB548579) was included as a reference strain and Staphylococcus aureus (JN102565) was included as an outgroup. KR-accession numbers correspond to gene sequences that belong to isolates analyzed in this study while AB548579 and JN102565 were obtained from the NCBI database. Bootstrap values above 50% are shown (1000 replications).

Figure 4

Neighbor joining tree based on 16S rRNA gene sequences of Staphylococcus aureus isolated from local radish. Enterococcus sulfureus ATCC 49903 (NR115766) was included as an outgroup. KR-accession numbers correspond to gene sequences that belong to isolates analyzed in this study while others were obtained from NCBI database. Bootstrap values above 50% are shown (1000 replications).

Figure 5

Neighbor joining tree based on sequencing 16S rRNA gene for members of Enterococcus isolated from fresh produce. Staphylococcus aureus (JN102565) was included as an outgroup. KR-accession numbers correspond to gene sequences that belong to isolates analyzed in this study while others were obtained from NCBI database. Bootstrap values above 50% are shown (1000 replications).