Comprehensive resistome analysis reveals the prevalence of NDM and MCR-1 in Chinese poultry production.
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 blaNDMand 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 blaNDMquickly 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 blaNDMand 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.
Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China.
Yang
Y
Wang
Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China.
Rongmin
R
Zhang
Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China.
Jiyun
J
Li
College of Veterinary Medicine, Iowa State University, Ames, Iowa 50011-1134, USA.
Zuowei
Z
Wu
Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China.
Wenjuan
W
Yin
Institute of Microbiology and Epizootics, Department of Veterinary Medicine, Freie Universität Berlin, 14163 Berlin, Germany.|Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, 31535 Neustadt-Mariensee, Germany.
Stefan
S
Schwarz
Department of Medical Microbiology and Infectious Disease, Institute of Infection &Immunity, UHW Main Building, Heath Park Hospital, Cardiff CF14 4XN, UK.
Jonathan M
JM
Tyrrell
College of Engineering, China Agricultural University, Beijing 100083, China.
Yongjun
Y
Zheng
Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China.
Shaolin
S
Wang
Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China.
Zhangqi
Z
Shen
Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, China Agricultural University, Beijing 100193, China.
Zhihai
Z
Liu
Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, China Agricultural University, Beijing 100193, China.
Jianye
J
Liu
Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, China Agricultural University, Beijing 100193, China.
Lei
L
Lei
Department of Medical Microbiology and Infectious Disease, Institute of Infection &Immunity, UHW Main Building, Heath Park Hospital, Cardiff CF14 4XN, UK.|Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, China Agricultural University, Beijing 100193, China.
Mei
M
Li
College of Animal Science and Technology, Qingdao Agricultural University, Qingdao 266109, Shandong, China.
Qidi
Q
Zhang
Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China.
Congming
C
Wu
College of Veterinary Medicine, Iowa State University, Ames, Iowa 50011-1134, USA.
Qijing
Q
Zhang
The Key Laboratory of Food Safety Risk Assessment, Ministry of Health and China National Center for Food Safety Risk Assessment, Beijing 100021, China.
Yongning
Y
Wu
Department of Medical Microbiology and Infectious Disease, Institute of Infection &Immunity, UHW Main Building, Heath Park Hospital, Cardiff CF14 4XN, UK.
Timothy R
TR
Walsh
Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China.
Jianzhong
J
Shen
D000818:Animals; D000835:Animals, Wild / Q000382:microbiology; D000900:Anti-Bacterial Agents / Q000494:pharmacology; D001717:Birds / Q000382:microbiology; D000073182:Carbapenem-Resistant Enterobacteriaceae / Q000187:drug effects / Q000235:genetics*; D002645:Chickens / Q000382:microbiology*; D002681:China / Q000453:epidemiology; D003091:Colistin / Q000494:pharmacology; D004175:Diptera / Q000382:microbiology; D004285:Dogs; D024881:Drug Resistance, Bacterial / Q000235:genetics*; D024901:Drug Resistance, Multiple, Bacterial / Q000235:genetics*; D004926:Escherichia coli / Q000187:drug effects / Q000235:genetics* / Q000302:isolation & purification; D004927:Escherichia coli Infections / Q000453:epidemiology / Q000382:microbiology; D029968:Escherichia coli Proteins / Q000235:genetics*; D016680:Genome, Bacterial; D059014:High-Throughput Nucleotide Sequencing; D008826:Microbial Sensitivity Tests; D015995:Prevalence; D001618:beta-Lactamases / Q000235:genetics*
D000900:Anti-Bacterial Agents; D029968:Escherichia coli Proteins; C000614037:MCR-1 protein, E coli; D001618:beta-Lactamases; D003091:Colistin