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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 producer 1 . 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 sector 2 . To understand the impact of banning colistin and the epidemiology of multi-drug-resistant (MDR) Escherichia coli (using bla NDM and mcr-1 as marker genes), we sampled poultry, dogs, sewage, wild birds and flies. Here, we show that mcr-1, but not bla NDM , is prevalent in hatcheries, but bla NDM 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 bla NDM and mcr-1 in hatcheries, commercial farms, a slaughterhouse and supermarkets revealed considerably higher levels of positive samples than the bla NDM - 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 bla NDM -positive E. coli shared among farms, flies, dogs and farmers, providing direct evidence of carbapenem-resistant E. coli transmission and environmental contamination.

Objectives: Characterization of non-Escherichia coli NDM-carrying Enterobacteriaceae in the poultry production environment.Methods: A total of 36 NDM-positive Enterobacteriaceae (22 Klebsiella pneumoniae, 13 Enterobacter cloacae and 1 Salmonella enterica) were isolated from a chicken farm and WGS was conducted using Illumina Hiseq2500. The genomic characterization of the isolates acquired through WGS analysis included the genomic context-flanking blaNDM genes, MLST, the antibiotic resistance genes (ARGs) and replicon types of plasmids. WGS information for another 73 K. pneumoniae isolates from different sources was retrieved from GenBank and then combined with isolates in this study for comparative genomic and phylogenetic analysis.Results: Three types of genetic environment carrying blaNDM were identified in 36 non-E. coli Enterobacteriaceae isolates. Sequence comparison analysis indicated these genetic environments were completely identical to our previous findings. WGS further revealed three major types of plasmids (IncFIB, IncX3 and IncFII) from these isolates and the phylogenetic analysis suggested several K. pneumoniae isolates with ST11, ST37 and ST147 from the commercial chicken farm that were closely related to isolates of human origin.Conclusions: The blaNDM-harbouring genetic contexts were identified not only in E. coli, but also in K. pneumoniae, E. cloacae and S. enterica, which may indicate that blaNDM has been widely disseminated to non-E. coli Enterobacteriaceae species in animal farms. The close relationship of K. pneumoniae isolates from different origins suggests they could serve as a key vehicle for the transfer of ARGs between humans and food animal production environments. [ABSTRACT FROM AUTHOR]

• C. perfringens was found in 23.4 % of chickens and 72.0 % of pigs. • All 322 C. perfringens isolates belonged to toxin type A and 45.7 % carried beta-2 toxin-encoding gene cpb2. • Most strains showed high-level resistance to gentamicin and sulfonamides, and low resistance to amoxicillin-clavulanate and cephalosporins. • Genetic diversity was observed and high nucleotide sequence identity to C. perfringens plasmids suggested that horizontal gene transfer may occur. • Isolates from the same farms and areas were found to be phylogenetically close. The prevalence and antimicrobial susceptibility of Clostridium perfringens (C. perfringens) in chickens and pigs were investigated in Beijing and Shanxi, China. In total, 322 C. perfringens (chicken n = 60 and pig n = 262) were obtained from 620 feces of chickens (n = 256) and pigs (n = 364). Multiplex PCR for toxin typing of C. perfringens revealed that all the isolates belong to type A, with 45.7 % (147/322) isolates carrying beta-2 toxin-encoding gene cpb2. Minimum inhibitory concentrations of 27 antimicrobial agents showed that 91.0 % of the tested C. perfringens isolates were resistant to gentamicin and sulfonamides (sulfisoxazole and trimethoprim-sulfamethoxazole), and little resistance was showed to amoxicillin-clavulanate, ceftiofur, doxycycline, vancomycin and linezolid. Additionally, nosiheptide, avilamycin, virginiamycin and bacitracin exhibited good activity against the tested C. perfringens with low MIC 50 (0.06 to ≤4 μg/mL) and MIC 90 values (0.25–8 μg/mL). Whole genome sequencing (WGS) of 48 representative isolates from each farm indicated that the C. perfringens contained diverse antimicrobial resistance genes [ tetA (P), ant(6)-Ib , erm (Q), etc.] and toxin genes (cpb2 , colA , cloSI , pfoA , etc.). By comparative analysis, four C. perfringens isolates from three different pig farms harboured cpb2 -carrying plasmid p1 with 100 % nucleotide sequence identity, suggesting horizontal gene transfer among these microorganisms. The further phylogenomic reconstruction, based on the core-genome single nucleotide polymorphisms (SNPs) of the representatives, demonstrating that C. perfringens from the same farms and regions were closely related. These findings expanded our knowledge of C. perfringens isolated from animals in China, which provided scientific basis for efficient intervention or prevention measures of antimicrobial resistance in animal husbandry in China. [ABSTRACT FROM AUTHOR]