Abstract
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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Acknowledgements
This work was supported in part by the National Natural Science Foundation of China (grant nos 31530076, 31422055 and 81661138002) and the National Key Basic Research Program of China (grant no. 2013CB127200). T.R.W. and J.M.T. were also supported by MRC grant DETER-XDR-CHINA (MR/P007295/1).
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The study was planned and directed by J.S. and T.R.W. Experiments were conducted by Y.Wang, R.Z., J.Li, W.Y., Z.L., Z.S., L.L. and M.L. Sampling was conducted by Y.Wang, R.Z., J.Li, J.Liu and Q-d.Z. Data analysis was performed by Z.W., S.S., Y.Z., S.W., J.M.T., C.W., Q-j.Z. and Y.Wu. The manuscript was prepared by J.S., T.R.W., Y.Wang and R.Z.
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Supplementary Figures 1 and 2; Supplementary Tables 1, 3, 4, 6 and 7. (PDF 1453 kb)
Supplementary Tables 2 and 5
Supplementary Table 2: Characterization of genome-sequenced E. coli isolates (n = 174, 161 CREC and 13 CSEC); Supplementary Table 5: MIC values of all E. coli isolates (n = 216, 161 CREC and 55 CSEC). (XLSX 33 kb)
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Wang, Y., Zhang, R., Li, J. et al. Comprehensive resistome analysis reveals the prevalence of NDM and MCR-1 in Chinese poultry production. Nat Microbiol 2, 16260 (2017). https://doi.org/10.1038/nmicrobiol.2016.260
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DOI: https://doi.org/10.1038/nmicrobiol.2016.260
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