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

Wang, Yang, Zhang, Rongmin, Li, Jiyun, Wu, Zuowei, Yin, Wenjuan, Schwarz, Stefan, Tyrrell, Jonathan M. ORCID:, Zheng, Yongjun, Wang, Shaolin, Shen, Zhangqi, Liu, Zhihai, Liu, Jianye, Lei, Lei, Li, Mei, Zhang, Qidi, Wu, Congming, Zhang, Qijing, Wu, Yongning, Walsh, Timothy R. ORCID: and Shen, Jianzhong 2017. Comprehensive resistome analysis reveals the prevalence of NDM and MCR-1 in Chinese poultry production. Nature Microbiology 2 , 16260. 10.1038/nmicrobiol.2016.260

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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.

Item Type: Article
Date Type: Published Online
Status: Published
Schools: Medicine
Publisher: Nature Research
ISSN: 2058-5276
Funders: MRC
Date of First Compliant Deposit: 21 July 2017
Date of Acceptance: 29 October 2016
Last Modified: 02 Nov 2022 11:40

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