The Human Gut Microbiome as a Transporter of Antibiotic Resistance Genes between Continents

Abstract

Previous studies of antibiotic resistance dissemination by travel have, by targeting only a select number of cultivable bacterial species, omitted most of the human microbiome. Here, we used explorative shotgun metagenomic sequencing to address the abundance of >300 antibiotic resistance genes in fecal specimens from 35 Swedish students taken before and after exchange programs on the Indian peninsula or in Central Africa. All specimens were additionally cultured for extended-spectrum beta-lactamase (ESBL)-producing enterobacteria, and the isolates obtained were genome sequenced. The overall taxonomic diversity and composition of the gut microbiome remained stable before and after travel, but there was an increasing abundance of Proteobacteria in 25/35 students. The relative abundance of antibiotic resistance genes increased, most prominently for genes encoding resistance to sulfonamide (2.6-fold increase), trimethoprim (7.7-fold), and beta-lactams (2.6-fold). Importantly, the increase observed occurred without any antibiotic intake. Of 18 students visiting the Indian peninsula, 12 acquired ESBL-producing Escherichia coli, while none returning from Africa were positive. Despite deep sequencing efforts, the sensitivity of metagenomics was not sufficient to detect acquisition of the low-abundant genes responsible for the observed ESBL phenotype. In conclusion, metagenomic sequencing of the intestinal microbiome of Swedish students returning from exchange programs in Central Africa or the Indian peninsula showed increased abundance of genes encoding resistance to widely used antibiotics.

FIG 1

Average fold change of resistance gene categories after travel (log₁₀ scale). Changes in the entire cohort significant after correction for multiple testing are indicated with an asterisk. Significance within the Indian peninsula or the Central Africa group is indicated with a plus sign.

FIG 2

Changes of resistance genes detected in at least 10 individuals. The diameter of each dot represents the magnitude of change in that individual (log₁₀ scale). Green indicates decreases, and red indicates increases. Changes significant after correction for multiple testing are indicated with asterisks, while changes only significant using the Wilcoxon signed-rank test (putatively changed genes) are indicated by circles.

FIG 3

Fold changes of resistance genes significantly changed after correction for multiple testing. All shown genes were significantly more abundant after travel, using correction for multiple testing when the two destinations were combined. Error bars represent standard error of the mean.

FIG 4

Abundance of beta-lactam resistance genes in all specimens (before and after). Specimens with ESBL-positive isolates are indicated by a plus sign. ESBL resistance gene names are shown in bold, while carbapenemase gene names are indicated in red. The diameter of each dot represents the relative abundance of that gene in that specimen (log₁₀ scale).

FIG 5

Resistance genes colocalized on the same assembled contig. Blue edges represent contigs from before specimens, green edges correspond to Central Africa after specimens, and orange edges indicate contigs from the Indian peninsula after specimens. Numbers show the percentage of individuals where the co-occurring genes were detected.