The intestinal microbiota predisposes to traveler's diarrhea and to the carriage of multidrug-resistant Enterobacteriaceae after traveling to tropical regions

Abstract

The risk of acquisition of multidrug-resistant Enterobacteriaceae (MRE) and of occurrence of diarrhea is high when traveling to tropical regions. The relationships between these phenomena and the composition of human gut microbiota have not yet been assessed. Here, we investigated the dynamics of changes of metabolically active microbiota by sequencing total RNA from fecal samples taken before and after travel to tropical regions. We included 43 subjects who could provide fecal samples before and after a travel to tropical regions. When found positive by culturing for any MRE after travel, the subjects sent an additional sample 1 month later. In all, 104 fecal samples were considered (43 before travel, 43 at return, 18 one month after travel). We extracted the whole RNA, performed retrotranscription and sequenced the cDNA (MiSeq 2x300bp). The reads were mapped to the reference operational taxonomic units (OTUs) and species/strains using the 16S Greengenes and 23S SILVA databases. We found that the occurrence of diarrhea during the travel was associated with a higher relative abundance of Prevotella copri before departure and after return. The composition of microbiota, before travel as well as at return, was not correlated with the acquisition of MRE. However, the clearance of MRE one month after return was linked to a specific pattern of bacterial species that was also found before and after return. In conclusion, we found specific OTUs associated to a higher risk of diarrhea during a stay in tropical regions and to a faster clearance of MRE after their acquisition.

Keywords: Multidrug-resistant Enterobacteriaceae; gut microbiota; traveller’s diarrhea; travelling to tropical regions.

Figure 1.

Microbiota changes with respect to the occurrence of diarrhea during the travel. (a) PCoA plot showing the distribution of samples taken at the return, from travelers who had (red triangles) or not (blue triangles) diarrhea during the travel. Of the 6 individuals who suffered from diarrhea 3 went to Asia, 2 to Sub-Saharan Africa and 1 to Latin America. Percentage of variation explained by the first two axes is indicated. (b) Boxplots and dot plots depicting the values and their corresponding distributions of ecological indexes, computed at the 16S OTU level, before travel (BT) and at return (AR), between travelers experiencing or not diarrhea. Stars correspond to the following p-values: * = <0.05; ** = <0.01; *** = <0.001. (c) Bar plots reporting the averaged relative abundance (/100) of phyla detected by mapping to 16S Greengenes database in travelers without diarrhea (n = 33 of which 11 were still MRE positive one month after the return) and those with (n = 6 of which 3 were still MRE positive one month after the return). Numbers at the top of the bars indicate the amount of samples for each travel time point/condition. (D) Bar plot reporting log10-transformed LDA scores of OTUs selected by LEfSe analyses (p-value <0.05). Cohorts of samples and colour label are the same as explained in (a). Only OTUs with the absolute value of LDA score (scaled in log10) of at least 3 are represented. Greengenes taxonomy identifiers for all OTUs are reported in Supplementary Table 4.

Figure 2.

Comparison of travelers who acquired MRE and remained positive (n = 11) or became negative (n = 6) one month after return. (a) Heat map illustrating the mean relative abundance (expressed as percentage of total reads) of 19 OTUs in the three sampling points (BT, AR and 1 mo. AR = before travel, at return and one month after the return, respectively) of travelers MRE positive (yellow bottom bar) and MRE negative (blue bottom bar) one month after the return. OTUs were selected if the p-value was < 0.05 (Wilcoxon rank sum test), the fold change was of at least 2, and when the mean relative abundance was of at least 0.1% in one of the six represented conditions represented (i.e. BT, AR and 1 mo. AR of MRE-positives and of MRE-negatives one month after the return). Greengenes taxonomy identifiers for all OTUs are reported in Supplementary Table 4. (b) Barplot reporting log10-transformed LDA scores from each OTUs resulting significant (p-value < 0.05) from LEfSe analyses on samples from travelers MRE positive (yellow) and MRE negative (blue) one month after the return. Only OTUs with an absolute value of LDA score (scaled in log10) of at least 2.5 were retained for graphic representation. (c) PCoA plot showing the distribution of samples from time points of travelers MRE negative and MRE positive one month after return. PCO1 (12.7%) and PCO2 (8%) represent the degrees of variance of each axis. Samples are grouped in clusters delimited by ellipses. Represented centroids (spheres) capture the origin of each ellipsis. (d) Bar plots reporting the averaged relative abundance (/100) of phyla detected by mapping to 16S Greengenes database in travelers MRE negative (n = 11) and MRE positive travelers (n = 6) one month after return.