The Bacterial Mobile Resistome Transfer Network Connecting the Animal and Human Microbiomes

Abstract

Horizontally acquired antibiotic resistance genes (ARGs) in bacteria are highly mobile and have been ranked as principal risk resistance determinants. However, the transfer network of the mobile resistome and the forces driving mobile ARG transfer are largely unknown. Here, we present the whole profile of the mobile resistome in 23,425 bacterial genomes and explore the effects of phylogeny and ecology on the recent transfer (≥99% nucleotide identity) of mobile ARGs. We found that mobile ARGs are mainly present in four bacterial phyla and are significantly enriched in Proteobacteria The recent mobile ARG transfer network, which comprises 703 bacterial species and 16,859 species pairs, is shaped by the bacterial phylogeny, while an ecological barrier also exists, especially when interrogating bacteria colonizing different human body sites. Phylogeny is still a driving force for the transfer of mobile ARGs between farm animals and the human gut, and, interestingly, the mobile ARGs that are shared between the human and animal gut microbiomes are also harbored by diverse human pathogens. Taking these results together, we suggest that phylogeny and ecology are complementary in shaping the bacterial mobile resistome and exert synergistic effects on the development of antibiotic resistance in human pathogens.

Importance: The development of antibiotic resistance threatens our modern medical achievements. The dissemination of antibiotic resistance can be largely attributed to the transfer of bacterial mobile antibiotic resistance genes (ARGs). Revealing the transfer network of these genes in bacteria and the forces driving the gene flow is of great importance for controlling and predicting the emergence of antibiotic resistance in the clinic. Here, by analyzing tens of thousands of bacterial genomes and millions of human and animal gut bacterial genes, we reveal that the transfer of mobile ARGs is mainly controlled by bacterial phylogeny but under ecological constraints. We also found that dozens of ARGs are transferred between the human and animal gut and human pathogens. This work demonstrates the whole profile of mobile ARGs and their transfer network in bacteria and provides further insight into the evolution and spread of antibiotic resistance in nature.

FIG 1

Heat map showing the distribution of mobile ARGs in different taxonomic ranks. Inner to outer circles indicate sequentially the phylum, class, order, family, genus, and species. Each bar in the outermost circle represents a species (n = 790), and the sizes of the other sectors representing different taxa are scaled according to the number of species assigned to that taxon. Scale bar, gene numbers. Species harboring more than 20 mobile ARGs are shown beside the species bars, and species with more than 40 ARGs are highlighted in bold. The phylogenetic affiliation is based on NCBI taxonomy.

FIG 2

Recent HGT networks of the mobile resistome. (A) The network of species sharing mobile ARGs. Each node represents a species, and the node sizes and the labels are scaled according to the number of mobile ARGs detected in that species. The edge between any two nodes indicates that there are at least 3 shared mobile ARGs (≥99% nucleotide identity) by the species pair, with greater thickness and width of the edge for a larger number of shared mobile ARGs. Nodes of the same color indicate species belonging to the same family, and the same shape denotes the same phylum. The entire profile of this network can be found in Fig. S4A in the supplemental material. (B) The network of mobile ARGs shared between species. Dots and triangles represent species (n = 703) and ARGs (n = 222), respectively. Edges linking species and ARGs indicate that the ARGs were shared among those species. The sizes of the gene labels are scaled based on the number of species harboring the gene. The names of the ARGs shared among less than 20 species are not labeled.

FIG 3

The HGT frequency of the mobile ARGs across phylogenetic hierarchies and ecologies. (A) Intra- and intertaxon HGT frequency of the mobile ARGs across human, animal, aquatic, and terrestrial environments. The phylogenetic affiliation was based on NCBI taxonomy. Statistical analysis was performed using the Mann-Whitney U test: **, P ≤ 0.01; ***, P ≤ 0.001. From left to right: phylum, class, order, family, and genus. (B) The 16S rRNA gene distance-based HGT frequency of the mobile ARGs across bacterial communities of different human body sites. The HGT frequency in panel B is calculated in bins of 2% 16S rRNA gene sequence divergence; the data shown are mean values, and light shading denotes the interquartile range (IQR) between the first and third quartiles. See Materials and Methods for the detailed calculation process.

FIG 4

Structures of human and animal gut bacterial communities are correlated with mobile ARG transfer. Bacterial composition at the phylum level (A) and the genus level (B). Correlation of the shared mobile ARG number with the similarity of the bacterial community at the phylum level (C) and the genus level (D).

FIG 5

Shared mobile ARGs among human and animal gut microbiomes and human pathogens. (A) Network of the shared mobile ARGs. Edges linking species/gut and ARGs indicate that the ARGs were shared among those species/gut microbiomes. Number of human pathogen species: n = 47; number of shared mobile ARGs between humans and animals: n = 41; number of shared mobile ARGs among humans, animals, and human pathogens: n = 33. Comparison of representative animal and human gut assembled contigs harboring the macrolide-lincosamide-streptogramin B resistance gene erm(F) (B) and the aminoglycoside resistance gene ant(6)-Ia (C) with representative human pathogen genomes and known mobile genetic elements.