MCR-1-positve Escherichia coli (MCRPEC) have been reported in humans worldwide; however, thus far, their prevalence is low and potential sources for human mcr-1 carriage have not yet been identified. Here, we analyse a nationwide epidemiological dataset on MCRPEC in humans throughout China and assess the factors associated with MCRPEC carriage using natural and national anthropogenic data. We identified 774 non-duplicate MCRPEC isolates from 774 stool samples collected from 5,159 healthy individuals in 30 provinces and municipalities in 2016, with a prevalence of MCRPEC ranging from 3.7 to 32.7% (average: 15.0%)—substantially higher than previously reported. MCRPEC carriage was associated with provincial regions, the production of sheep and freshwater aquaculture, annual consumption of total meat, pork and mutton, and daily intake of aquaculture products. MCRPEC was significantly more prevalent in provinces with higher aquaculture industries. Whole-genome sequencing analysis revealed that the MCRPEC isolates were clustered into four distinct lineages, two of which were dominant and harboured most of the MCRPEC isolates. The high prevalence of MCRPEC in the community poses a substantial risk for colistin usage in clinical practice and suggests the need for intestinal screening of mcr-1 carriers in intensive care units in Chinese hospitals. Furthermore, our data suggest that aquaculture is a significant reservoir of mcr-1.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Additional information

Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Change history

  • 03 August 2018

    An incorrect Reporting Summary was originally published with this Article; this has now been replaced with the correct file.


  1. 1.

    Liu, Y. Y. et al. Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China: a microbiological and molecular biological study. Lancet Infect. Dis. 16, 161–168 (2016).

  2. 2.

    Wang, Y. et al. Prevalence, risk factors, outcomes, and molecular epidemiology of mcr-1-positive Enterobacteriaceae in patients and healthy adults from China: an epidemiological and clinical study. Lancet Infect. Dis. 17, 390–399 (2017).

  3. 3.

    Di Pilato, V. et al. mcr-1.2, a new mcr variant carried on a transferable plasmid from a colistin-resistant KPC carbapenemase-producing Klebsiella pneumoniae strain of sequence type 512. Antimicrob. Agents Chemother. 60, 5612–5615 (2016).

  4. 4.

    Bai, L. et al. A novel disrupted mcr-1 gene and a lysogenized phage P1-like sequence detected from a large conjugative plasmid, cultured from a human atypical enteropathogenic Escherichia coli (aEPEC) recovered in China. J. Antimicrob. Chemother. 72, 1531–1533 (2017).

  5. 5.

    Tijet, N. et al. Molecular characteristics of mcr-1-carrying plasmids and new mcr-1 variant recovered from polyclonal clinical Escherichia coli from Argentina and Canada. PLoS ONE 12, e0180347 (2017).

  6. 6.

    Lu, X. et al. MCR-1.6, a new MCR variant carried by an IncP plasmid in a colistin-resistant Salmonella enterica serovar Typhimurium isolate from a healthy individual.Antimicrob. Agents Chemother. 61, e02632-16 (2017).

  7. 7.

    Poirel, L., Jayol, A. & Nordmann, P. Polymyxins: antibacterial activity, susceptibility testing, and resistance mechanisms encoded by plasmids or chromosomes. Clin. Microbiol. Rev. 30, 557–596 (2017).

  8. 8.

    Walsh, T. R. & Wu, Y. N. China bans colistin as a feed additive for animals. Lancet Infect. Dis. 16, 1102–1103 (2016).

  9. 9.

    Schwarz, S. & Johnson, A. P. Transferable resistance to colistin: a new but old threat. J. Antimicrob. Chemother. 71, 2066–2070 (2016).

  10. 10.

    Wang, X. et al. Molecular epidemiology of colistin-resistant Enterobacteriaceae in inpatient and avian isolates from China: high prevalence of mcr-negative Klebsiella pneumoniae. Int. J. Antimicrob. Agents 50, 536–541 (2017).

  11. 11.

    Quan, J. et al. Prevalence of mcr-1 in Escherichia coli and Klebsiella pneumoniae recovered from bloodstream infections in China: a multicentre longitudinal study. Lancet Infect. Dis. 17, 400–410 (2017).

  12. 12.

    Terveer, E. M. et al. Prevalence of colistin resistance gene (mcr-1) containing Enterobacteriaceae in feces of patients attending a tertiary care hospital and detection of a mcr-1 containing, colistin susceptible E. coli. PLoS ONE 12, e0178598 (2017).

  13. 13.

    Bi, Z. et al. Prevalence of the mcr-1 colistin resistance gene in extended-spectrum β-lactamase-producing Escherichia coli from human faecal samples collected in 2012 in rural villages in Shandong Province, China. Int. J. Antimicrob. Agents 49, 493–497 (2017).

  14. 14.

    Zhong, L. L. et al. High rates of human fecal carriage of mcr-1-positive multi-drug resistant Enterobacteriaceae isolates emerge in China in association with successful plasmid families.Clin. Infect. Dis. 66, 676–685 (2017).

  15. 15.

    Wang, Y. et al. Comprehensive resistome analysis reveals the prevalence of NDM and MCR-1 in Chinese poultry production. Nat. Microbiol. 2, 16260 (2017).

  16. 16.

    Bernasconi, O. J. et al. Travelers can import colistin-resistant Enterobacteriaceae, including those possessing the plasmid-mediated mcr-1 gene. Antimicrob. Agents Chemother. 60, 5080–5084 (2016).

  17. 17.

    Cabello, F. C., Godfrey, H. P., Buschmann, A. H. & Dolz, H. J. Aquaculture as yet another environmental gateway to the development and globalisation of antimicrobial resistance. Lancet Infect. Dis. 16, e127–e133 (2016).

  18. 18.

    Cabello, F. C., Tomova, A., Ivanova, L. & Godfrey, H. P. Aquaculture and mcr colistin resistance determinants. mBio 8, e01229-17 (2017).

  19. 19.

    Yao, C. S. et al. Geographical agglomeration characteristic and spatial evolution mechanism of aquaculture industry in China [article in Chinese]. Econ. Geogr. 36, 118–127 (2016).

  20. 20.

    Wu, C. et al. Rapid rise of the ESBL and mcr-1 genes in Escherichia coli of chicken origin in China, 2008–2014.Emerg. Microbes Infect. 7, 30 (2018).

  21. 21.

    Sato, H., Ouchi, M. & Koumi, J. Distribution of colistin sulfate in the body. Distribution and metabolism of orally administered colistin sulfate in chickens and pigs [article in Japenase]. Jpn J. Antibiot. 25, 239–245 (1972).

  22. 22.

    Rhouma, M. et al. Gastric stability and oral bioavailability of colistin sulfate in pigs challenged or not with Escherichia coli O149: F4 (K88). Res. Vet. Sci. 102, 173–181 (2015).

  23. 23.

    Li, J., Milne, R. W., Nation, R. L., Turnidge, J. D. & Coulthard, K. Stability of colistin and colistin methanesulfonate in aqueous media and plasma as determined by high-performance liquid chromatography. Antimicrob. Agents Chemother. 47, 1364–1370 (2003).

  24. 24.

    Qiong, C. & Ji-min, W. Current situation and future trends of meat consumption in China [ariticle in Chinese]. Food Nutr. China 19, 43–47 (2013).

  25. 25.

    Zhou, H. W. et al. Occurrence of plasmid- and chromosome-carried mcr-1 in waterborne Enterobacteriaceae in China.Antimicrob. Agents Chemother. 61, e00017-17 (2017).

  26. 26.

    Fernandes, M. R. et al. Colistin-resistant mcr-1-positive Escherichia coli in public beaches, an infectious threat emerging in recreational waters.Antimicrob. Agents Chemother. 61, e00234-17 (2017).

  27. 27.

    Hu, Y. Y. et al. Colistin-resistance gene mcr-1 in children’s gut flora.Int. J. Antimicrob. Agents 50, 593–597 (2017).

  28. 28.

    M100-S25: Performance Standards for Antimicrobial Susceptibility Testing; Twenty-Fifth Informational Supplement (Clinical and Laboratory Standards Institute, 2015).

  29. 29.

    Bankevich, A. et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455–477 (2012).

  30. 30.

    Inouye, M. et al. SRST2: rapid genomic surveillance for public health and hospital microbiology labs. Genome Med. 6, 90 (2014).

  31. 31.

    Treangen, T. J., Ondov, B. D., Koren, S. & Phillippy, A. M. The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes. Genome Biol. 15, 524 (2014).

  32. 32.

    Letunic, I. & Bork, P. Interactive tree of life (iTOL)v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res. 44, W242–W245 (2016).

  33. 33.

    Cheng, L., Connor, T. R., Siren, J., Aanensen, D. M. & Corander, J. Hierarchical and spatially explicit clustering of DNA sequences with BAPS software. Mol. Biol. Evol. 30, 1224–1228 (2013).

  34. 34.

    Carattoli, A. et al. In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob. Agents Chemother. 58, 3895–3903 (2014).

Download references


This work was supported in part by grants from the National Key Research and Development Program of China (2018YFD0500300), National Natural Science Foundation of China (81661138002 and 81772250) and Medical Research Council grant DETER-XDRE-CHINA (MR/P007295/1).

Author information

Author notes

  1. These authors contributed equally: Yingbo Shen, Hongwei Zhou.


  1. Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China

    • Yingbo Shen
    • , Yongqiang Wang
    • , Bing Shao
    • , Congming Wu
    • , Lu Yang
    • , Zhangqi Shen
    • , Yanran Ou
    • , Shaolin Wang
    • , Jianzhong Shen
    •  & Yang Wang
  2. The Second Affiliated Hospital of Zhejiang University, Zhejiang University, Hangzhou, China

    • Hongwei Zhou
    • , Yanyan Hu
    • , Qiaoling Sun
    •  & Rong Zhang
  3. Institute for Nutrition and Health, Chinese Center for Disease Control and Prevention, Beijing, China

    • Jiao Xu
  4. College of Veterinary Medicine, Iowa State University, Ames, IA, USA

    • Qijing Zhang
    •  & Zuowei Wu
  5. Department of Medical Microbiology and Infectious Disease, Institute of Infection and Immunity, Cardiff, UK

    • Timothy R. Walsh
  6. Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China

    • Yueling Wang
  7. Key Laboratory of Food Safety Risk Assessment, Ministry of Health and China National Center for Food Safety Risk Assessment, Beijing, China

    • Yongning Wu
  8. Australia-China Joint Laboratory for Animal Health Big Data Analytics, School of Veterinary and Life Sciences, Murdoch University, Murdoch, Australia

    • Chang Cai
  9. State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China

    • Juan Li
  10. Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China

    • Jianzhong Shen
    •  & Yang Wang


  1. Search for Yingbo Shen in:

  2. Search for Hongwei Zhou in:

  3. Search for Jiao Xu in:

  4. Search for Yongqiang Wang in:

  5. Search for Qijing Zhang in:

  6. Search for Timothy R. Walsh in:

  7. Search for Bing Shao in:

  8. Search for Congming Wu in:

  9. Search for Yanyan Hu in:

  10. Search for Lu Yang in:

  11. Search for Zhangqi Shen in:

  12. Search for Zuowei Wu in:

  13. Search for Qiaoling Sun in:

  14. Search for Yanran Ou in:

  15. Search for Yueling Wang in:

  16. Search for Shaolin Wang in:

  17. Search for Yongning Wu in:

  18. Search for Chang Cai in:

  19. Search for Juan Li in:

  20. Search for Jianzhong Shen in:

  21. Search for Rong Zhang in:

  22. Search for Yang Wang in:


Yang Wang, R.Z. and J.S. designed the study. Y.S., H.Z., J.X., Y.H., L.Y., Q.S., Y.O., Yue Wang and B.S. collected the data. Y.S., Yang Wang, Yong Wang, H.Z., R.Z., Q.Z., C.W., B.S., Z.S., Z.W., S.W., Y.Wu, C.C., J.L., T.R.W. and J.S. analysed and interpreted the data. Yang Wang, R.Z., Y.S. and T.R.W. wrote the manuscript. All authors reviewed, revised and approved the final report.

Competing interests

The authors declare no competing interests.

Corresponding authors

Correspondence to Jianzhong Shen or Rong Zhang or Yang Wang.

Supplementary information

  1. Supplementary Information

    Supplementary Figures 1–5, Supplementary Tables 4 and 5.

  2. Reporting Summary

  3. Supplementary Table 1

    Prevalence of mcr-1-positive samples and corresponding selected isolates for sequencing from 30 provinces in China.

  4. Supplementary Table 2

    Precipitation and anthropogenic data of 30 provinces in China.

  5. Supplementary Table 3

    MIC profiles of MCRPEC.

  6. Supplementary Table 6

    Characterization of 287 sequenced mcr-1-positive E. coli isolates.

About this article

Publication history