Extensive cross-species transmission of pathogens and antibiotic resistance genes in mammals neglected by public health surveillance

Yuqi Shi¹, Yuxing Li¹, Haipeng Li¹, Ayidana Haerheng¹, Vanessa R Marcelino², Meng Lu¹, Philippe Lemey³, Jia Tang¹, Yuhai Bi⁴, John H-O Pettersson⁵, Jon Bohlin⁶, Joon Klaps³, Zuowei Wu⁷, Wenbo Wan¹, Bowen Sun¹, Mei Kang¹, Edward C Holmes⁸, Na He¹, Shuo Su⁹

Affiliations

¹ Department of Epidemiology, School of Public Health, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China.
² Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia; Melbourne Integrative Genomics, School of Biosciences, University of Melbourne, Melbourne, VIC, Australia.
³ Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, Leuven, Belgium.
⁴ CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China.
⁵ Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia; Zoonosis Science Center, Clinical Microbiology, Department of Medical Sciences, University of Uppsala, Uppsala, Sweden; Department of Microbiology, Swedish Veterinary Agency, Uppsala, Sweden.
⁶ Norwegian Institute of Public Health, Domain for Infection Control, Section for Modeling and Bioinformatics, Oslo, Norway; Center for Fertility and Health, Norwegian Institute of Public Health, P.O. Box 222 Skøyen, Oslo, Norway.
⁷ Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA , USA.
⁸ School of Medical Sciences, The University of Sydney, Sydney, NSW, Australia; Laboratory of Data Discovery for Health Limited, Hong Kong SAR, China.
⁹ Department of Epidemiology, School of Public Health, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China. Electronic address: ssh5658485@163.com.

PMID: 40865528
DOI: 10.1016/j.cell.2025.08.016

Extensive cross-species transmission of pathogens and antibiotic resistance genes in mammals neglected by public health surveillance

Yuqi Shi et al. Cell. 2025.

. 2025 Aug 26:S0092-8674(25)00971-7.

doi: 10.1016/j.cell.2025.08.016. Online ahead of print.

Authors

Affiliations

¹ Department of Epidemiology, School of Public Health, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China.
² Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia; Melbourne Integrative Genomics, School of Biosciences, University of Melbourne, Melbourne, VIC, Australia.
³ Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, Leuven, Belgium.
⁴ CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China.
⁵ Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia; Zoonosis Science Center, Clinical Microbiology, Department of Medical Sciences, University of Uppsala, Uppsala, Sweden; Department of Microbiology, Swedish Veterinary Agency, Uppsala, Sweden.
⁶ Norwegian Institute of Public Health, Domain for Infection Control, Section for Modeling and Bioinformatics, Oslo, Norway; Center for Fertility and Health, Norwegian Institute of Public Health, P.O. Box 222 Skøyen, Oslo, Norway.
⁷ Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA , USA.
⁸ School of Medical Sciences, The University of Sydney, Sydney, NSW, Australia; Laboratory of Data Discovery for Health Limited, Hong Kong SAR, China.
⁹ Department of Epidemiology, School of Public Health, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China. Electronic address: ssh5658485@163.com.

PMID: 40865528
DOI: 10.1016/j.cell.2025.08.016

Abstract

Non-traditional farmed and wild mammals are often neglected in pathogen surveillance. Through metagenomic and metatranscriptomic sequencing of fecal and tissue samples from 973 asymptomatic mammals, we identified 128 viruses (30 novel), including a new coronavirus genus, 10,255 bacterial species (over 7,000 undescribed), 201 fungi, and 7 parasites. Farmed and wild mammals shared 13.3% of virus species, including canine coronavirus in Asiatic black bears and Getah virus in rabbits, while the 2.3.4.4b clade of H5N1 avian influenza virus was found in a wild leopard cat. We identified potential bacterial pathogen transmission between farmed and wild mammals and bacterial strains with high genetic similarity to those found in humans. We observed 157 clinically prioritized antibiotic resistance genes (ARGs) in mammalian microbiomes with greater than 99% identity to ARGs from human microbiomes, often co-occurring with mobile genetic elements. Overall, this work highlights cross-species risks at the human-animal interface.

Keywords: Getah virus; antibiotic resistance; avian influenza virus; cross-species transmission; microbial surveillance; mobile genetic element; unexported bacterial diversity.

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Conflict of interest statement

Declaration of interests The authors declare no competing interests.

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Extensive cross-species transmission of pathogens and antibiotic resistance genes in mammals neglected by public health surveillance

Affiliations

Extensive cross-species transmission of pathogens and antibiotic resistance genes in mammals neglected by public health surveillance

Authors

Affiliations

Abstract

Conflict of interest statement

LinkOut - more resources

Full Text Sources

Miscellaneous