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

Yang Wang, Rongmin Zhang, Jiyun Li, Zuowei Wu, Wenjuan Yin, Stefan Schwarz, Jonathan M Tyrrell, Yongjun Zheng, Shaolin Wang, Zhangqi Shen, Zhihai Liu, Jianye Liu, Lei Lei, Mei Li, Qidi Zhang, Congming Wu, Qijing Zhang, Yongning Wu, Timothy R Walsh, Jianzhong Shen

Research output: Contribution to journalArticle (Academic Journal)


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.

Original languageEnglish
Pages (from-to)16260
JournalNature Microbiology
Publication statusPublished - 6 Feb 2017


  • Animals
  • Animals, Wild/microbiology
  • Anti-Bacterial Agents/pharmacology
  • Birds/microbiology
  • Carbapenem-Resistant Enterobacteriaceae/drug effects
  • Chickens/microbiology
  • China/epidemiology
  • Colistin/pharmacology
  • Diptera/microbiology
  • Dogs
  • Drug Resistance, Bacterial/genetics
  • Drug Resistance, Multiple, Bacterial/genetics
  • Escherichia coli/drug effects
  • Escherichia coli Infections/epidemiology
  • Escherichia coli Proteins/genetics
  • Genome, Bacterial
  • High-Throughput Nucleotide Sequencing
  • Microbial Sensitivity Tests
  • Prevalence
  • beta-Lactamases/genetics

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  • Cite this

    Wang, Y., Zhang, R., Li, J., Wu, Z., Yin, W., Schwarz, S., Tyrrell, J. M., Zheng, Y., Wang, S., Shen, Z., Liu, Z., Liu, J., Lei, L., Li, M., Zhang, Q., Wu, C., Zhang, Q., Wu, Y., Walsh, T. R., & Shen, J. (2017). Comprehensive resistome analysis reveals the prevalence of NDM and MCR-1 in Chinese poultry production. Nature Microbiology, 2, 16260.