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Nat Microbiol. 2017 Feb 6;2:16260. doi: 10.1038/nmicrobiol.2016.260.

Comprehensive resistome analysis reveals the prevalence of NDM and MCR-1 in Chinese poultry production.

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Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China.
College of Veterinary Medicine, Iowa State University, Ames, Iowa 50011-1134, USA.
Institute of Microbiology and Epizootics, Department of Veterinary Medicine, Freie Universit├Ąt Berlin, 14163 Berlin, Germany.
Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, 31535 Neustadt-Mariensee, Germany.
Department of Medical Microbiology and Infectious Disease, Institute of Infection &Immunity, UHW Main Building, Heath Park Hospital, Cardiff CF14 4XN, UK.
College of Engineering, China Agricultural University, Beijing 100083, China.
Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, China Agricultural University, Beijing 100193, China.
College of Animal Science and Technology, Qingdao Agricultural University, Qingdao 266109, Shandong, China.
The Key Laboratory of Food Safety Risk Assessment, Ministry of Health and China National Center for Food Safety Risk Assessment, Beijing 100021, China.


By 2030, the global population will be 8.5 billion, placing pressure on international poultry production, of which China is a key producer1. From April 2017, China will implement the withdrawal of colistin as a growth promoter, removing over 8,000 tonnes per year from the Chinese farming sector2. To understand the impact of banning colistin and the epidemiology of multi-drug-resistant (MDR) Escherichia coli (using blaNDM and mcr-1 as marker genes), we sampled poultry, dogs, sewage, wild birds and flies. Here, we show that mcr-1, but not blaNDM, is prevalent in hatcheries, but blaNDM quickly contaminates flocks through dogs, flies and wild birds. We also screened samples directly for resistance genes to understand the true breadth and depth of the environmental and animal resistome. Direct sample testing for blaNDM and mcr-1 in hatcheries, commercial farms, a slaughterhouse and supermarkets revealed considerably higher levels of positive samples than the blaNDM- and mcr-1-positive E. coli, indicating a substantial segment of unseen resistome-a phenomenon we have termed the 'phantom resistome'. Whole-genome sequencing identified common blaNDM-positive E. coli shared among farms, flies, dogs and farmers, providing direct evidence of carbapenem-resistant E. coli transmission and environmental contamination.

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