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 Marcelino2,3
Meng Lu1
Philippe Lemey4
Jia Tang1
Yuhai Bi5
John H-O Pettersson2,6,7
Jon Bohlin8,9
Joon Klaps4
Zuowei Wu10
Wenbo Wan1
Bowen Sun1
Mei Kang1
Edward C Holmes11,12
Na He1
Shuo Su13
Affiliations13 institutions
Department of Epidemiology, School of Public Health, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China.
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.
Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, Leuven, Belgium.
CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China.
Zoonosis Science Center, Clinical Microbiology, Department of Medical Sciences, University of Uppsala, Uppsala, Sweden
Department of Microbiology, Swedish Veterinary Agency, Uppsala, Sweden.
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.
Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA , USA.
School of Medical Sciences, The University of Sydney, Sydney, NSW, Australia
Laboratory of Data Discovery for Health Limited, Hong Kong SAR, China.
Department of Epidemiology, School of Public Health, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China. Electronic address: [email protected].
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.
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.
Metagenomic sequencing identified 30 novel viruses, including a new coronavirus genus, showing genomic evidence of viral evolution in diverse mammalian hosts.
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.
