Integrated metagenome-resolved profiling of the resistome, virulome, and mobilome in the gut microbiota of wild birds

Su, J.; Gao, Y.-Q.; Elsheikha, H. M.; Lei, C.-C.; Xie, H.-L.; Nan, F.-L.; Ma, H.; Yang, M.-T.; Wang, H.-T.; Ni, H.-B.; Sun, H.-T.; Hongchao, S.; Zhang, X.-X.

doi:10.1101/2025.07.09.663844

bioRxiv · 10.1101/2025.07.09.663844

Integrated metagenome-resolved profiling of the resistome, virulome, and mobilome in the gut microbiota of wild birds

Su, J.·Gao, Y.-Q.·Elsheikha, H. M.·Lei, C.-C.·Xie, H.-L.·Nan, F.-L.·Ma, H.·Yang, M.-T.·Wang, H.-T.·Ni, H.-B.·Sun, H.-T.·Hongchao, S.·Zhang, X.-X.

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Abstract

Wild birds, with their extensive geographic distributions and high mobility, are increasingly recognized as important players in the dissemination of antimicrobial resistance. Their gut microbiota, shaped by exposure to diverse environments, may act as both reservoirs and vectors of antibiotic resistance genes (ARGs), virulence factor genes (VFGs), and mobile genetic elements (MGEs). In this study, we reconstructed 2,516 high-quality metagenome-assembled genomes (MAGs) from 718 gut metagenomes of wild birds to comprehensively profile their resistome and virulome. We identified 5,596 ARG-encoding proteins across 389 distinct ARG types, with multidrug resistance emerging as the most dominant category. Escherichia coli was the principal carrier of ARGs, and genes conferring resistance to elfamycin antibiotics via target alteration were notably widespread--indicating persistent antibiotic selection pressures in avian habitats. Co-occurrence analyses revealed extensive genetic linkage between ARGs, VFGs, and MGEs. Critically, we detected 25 ARG-MGE co-localization events within 5-kilobase genomic regions, highlighting a strong potential for horizontal gene transfer and accelerated resistance dissemination within microbial communities. Of particular concern was the detection of the tetX1 gene--conferring resistance to tigecycline, a last-resort antibiotic--in the gut microbiota of Chroicocephalus ridibundus and Cygnus cygnus. This finding strongly implicates anthropogenic pollution in the spread of clinically relevant ARGs into wildlife and emphasizes the risk of environmental transmission to other hosts, including humans. These results underscore the critical ecological role of wild birds in the global antimicrobial resistance network. As both reservoirs and potential vectors of ARGs, they represent a significant but under-monitored interface between environmental and clinical resistance pathways. Enhanced surveillance and mitigation strategies targeting wildlife are urgently needed to curb the environmental propagation of antimicrobial resistance.

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Su, J., Gao, Y.-Q., Elsheikha, H. M., Lei, C.-C., Xie, H.-L., Nan, F.-L., Ma, H., Yang, M.-T., Wang, H.-T., Ni, H.-B., Sun, H.-T., Hongchao, S., Zhang, X.-X.. 2025-07-09. Integrated metagenome-resolved profiling of the resistome, virulome, and mobilome in the gut microbiota of wild birds. https://doi.org/10.1101/2025.07.09.663844

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