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Volume 23, Number 7—July 2017

Locally Acquired mcr-1 in Escherichia coli, Australia, 2011 and 2013

Justin A. Ellem, Andrew N. Ginn, Sharon C.-A. Chen, John Ferguson, Sally R. Partridge, and Jonathan R. IredellComments to Author 
Author affiliations: Westmead Hospital, Westmead, New South Wales, Australia (J.A. Ellem, A.N. Ginn, S.C.-A. Chen, S.R. Partridge, J.R Iredell); New South Wales Health Pathology, Westmead (J.A. Ellem, A.N. Ginn, S.C.-A. Chen, J.R. Iredell); The University of Sydney, Sydney, New South Wales, Australia (A.N. Ginn, S.C.-A. Chen, S.R. Partridge, J.R. Iredell); The Westmead Institute for Medical Research, Westmead (A.N. Ginn, S.R. Partridge, J.R. Iredell); John Hunter Hospital, Newcastle, New South Wales, Australia (J. Ferguson); Pathology North, Newcastle (J. Ferguson); University of Newcastle, Newcastle (J. Ferguson)

Cite This Article


We identified discrete importation events of the mcr-1 gene on incompatibility group IncI2 plasmids in Escherichia coli isolated from patients in New South Wales, Australia, in 2011 and 2013. mcr-1 is present in a small minority of colistin-resistant Enterobacteriaceae and appears not to be established locally.

The mcr-1 (mobile colistin resistance) gene was discovered in Escherichia coli isolates collected during 2011–2014 from animals and meat products and from Klebsiella pneumoniae from human patients in China (1). Since then, mcr-1 has been identified on plasmids of various incompatibility (Inc) types associated with 0, 1, or 2 copies of the insertion sequence (IS) ISApl1 (2), and it has been identified in other species (most notably Salmonella spp.) and in several other countries (3), not including Australia. We analyzed colistin resistance in Enterobacteriaceae isolates collected in Sydney, New South Wales, Australia, during 2007–2016.

The Study

We reviewed 4,555 isolates of the family Enterobacteriaceae from 2007–2016 that were available for further testing for colistin (polymyxin E) resistance, excluding species that are intrinsically resistant. These isolates were from specimens tested at or referred to the Centre for Infectious Diseases Microbiology Laboratory Services at Westmead Hospital, Sydney, New South Wales, Australia, and were all resistant to third-generation cephalosporins, carbapenems, or both. For antimicrobial drug susceptibility testing, we used the Phoenix Automated Microbiology System (panels NMIC/ID-80, NMIC/ID-101, and NMIC-203; Becton Dickinson, Franklin Lakes, NJ, USA). Of the 4,555 isolates, 96 (2.1%) had a colistin (polymyxin E) minimum inhibitory concentration (MIC) of >2 μg/mL, which corresponds to EUCAST (European Committee on Antimicrobial Susceptibility Testing) breakpoints ( The 96 colistin-resistant isolates consisted of 44 K. pneumoniae, 8 K. oxytoca, 18 E. coli, 19 Enterobacter spp., 5 Hafnia alvei, and 2 Citrobacter freundii isolates. By using published primers (1), we identified mcr-1 in 2 of the colistin-resistant E. coli isolates; these isolates were from patients in different cities in New South Wales.

In September 2011, E. coli JIE2288 (colistin MIC of 4 μg/mL) was isolated from the urine of a 70-year-old woman after she had been in the intensive care unit (ICU) at Westmead Hospital, a large metropolitan hospital, for 2 months for management of a subarachnoid hemorrhage. The woman was not administered colistin/polymyxin antimicrobial drugs during hospitalization. The E. coli JIE2288 isolate was also resistant to amikacin, gentamicin, tobramycin, amoxicillin/clavulanic acid, cefotaxime, ceftazidime, cefepime, cefoxitin, trimethoprim/sulfamethoxazole, and ciprofloxacin, according to EUCAST breakpoints. The isolate was susceptible to piperacillin/tazobactam (MIC of <4/4 μg/mL) and meropenem (MIC of <1 μg/mL). The patient had no history of overseas travel in the previous 5 years, and while she was in the ICU, no other ICU patients had a recognized colistin-resistant infection and none were receiving colistin treatment. The patient was housed in a single room, and standard infection-control precautions (disposable gown and gloves) were used. The patient was treated with a course of meropenem, and subsequent cultures of her urine did not contain colistin-resistant E. coli.

In July 2013, a second colistin-resistant E. coli strain (herein designated JIE3685; colistin MIC of >4 μg/mL) was referred to our laboratory after being isolated from the urine of a 71-year-old woman with diabetes mellitus. The woman had sought care from a community physician in Newcastle, New South Wales, for a urinary tract infection. She had had no healthcare contact in the previous 2 years and no history of travel outside Australia in the previous 5 years. JIE3685 was also resistant to cefotaxime, cefepime, ciprofloxacin, gentamicin, tobramycin, and trimethoprim/sulfamethoxazole, but it was susceptible to amoxicillin/clavulanic acid, ceftazidime, piperacillin/tazobactam, meropenem, and amikacin.

We obtained colistin-resistant transconjugants from E. coli JIE2288 and JIE3685 essentially as previously described (4) and, using PCR, confirmed that they carried mcr-1. We subjected DNA prepared from the original JIE2288 and JIE3685 isolates and transconjugants to paired-end sequencing (NextSeq 500 platform; Illumina, San Diego, CA, USA) and assembled the sequences by using SPAdes 3.7.1 ( Using PlasmidFinder (, we identified IncI2 replicons in both isolates, and using the MLST tool on the Centre for Genomic Epidemiology website (, we identified JIE2288 as sequence type (ST) 167 (clonal complex [CC] 10) and JIE3865 as ST93 (CC168). Other ST167 isolates carrying mcr-1 have been reported; for example, mcr-1 was carried on a ≈65-kb IncI2 plasmid and the blaNDM-9 gene on a different plasmid in an isolate from chicken meat in China in 2014 (5). Furthermore, ST93 (CC168) is a known zoonotic pathogenic strain previously associated with transmission of mcr-1 from animals to humans in Laos (6) and China (7).

Most of the IncI2 plasmid from E. coli JIE2288 that carries mcr-1 (designated pJIE2288-1) was assembled as a single contig, missing only the shufflon region that rearranges to change the end of the pilV gene (8), causing assembly issues that may result in apparent differences between plasmids carrying mcr-1 (9). We obtained the shufflon segments of pJIE2288-1 by mapping raw reads to individual shufflon segments from the archetypal IncI2 plasmid R721 (GenBank accession no. AP002527) and then assembled them in the same order as in R721 to generate a complete plasmid sequence (8). An additional plasmid, carrying the blaCTX-M-14a gene (IncI1, designated pJIE2288-2), was identified in JIE2288. BLAST ( searches with 2 contigs from JIE3685 identified several closely matching plasmids (Table). We used pEC5-1, which had been sequenced by long-read methods, as a reference to resolve a repeated region and as a template for the shufflon, thus enabling complete assembly of a plasmid designated pJIE3685-1. We submitted the sequences of pJIE2288-1 and pJIE3685-1 to GenBank under accession numbers KY795977 and KY795978, respectively.

pJIE2288-1 and pJIE3685-1 each carry mcr-1 as the only resistance gene (located in the same position), and both lack ISApl1, but they do have differences in the remainder of their IncI2 backbones. pJIE2288-1 (60.733 kb) is closely related to 9 other sequenced mcr-1 plasmids (differing by only a few single nucleotide changes in backbone regions), some of which carry ISApl1 upstream of mcr-1, another IS, or both (Table). pJIE3685-1 (60.960 kb) is closely related to 6 other IncI2 mcr-1 plasmids (again, differing by only a few single nucleotide changes), all of which also lack ISApl1 (Table).


Thumbnail of Differences in promoter and ribosome binding site regions of mcr-1 in plasmids from Escherichia coli in Australia (indicated by arrows) and in other sequences available from GenBank. The sequences end with the ATG start codon of mcr-1 and a second ATG codon that follows it. The −35 and −10 regions of the proposed promoter (11) are indicated by arrows. The numbers to the right indicate how many times each variant has been seen among available sequences.

Figure. Differences in promoter and ribosome binding site regions of mcr-1 in plasmids from Escherichia coli in Australia (indicated by arrows) and in other sequences available from GenBank. The sequences end with...

We noted differences between pJIE2288-1 and pJIE3685-1 in the mcr-1 promoter (11) and putative ribosome binding site and these or other differences in this region in available mcr-1 sequences (Figure). We examined the chromosomal arnBCADTEF, pmrAB, and phoPQ genes of each isolate but did not identify any of the changes previously reported in association with colistin resistance in E. coli (12). This finding suggests that mcr-1 may be the sole phenotype determinant in these 2 strains.


We describe 2 E. coli isolates collected from patients in different cities in Australia ≈2 years apart that belong to STs previously associated with mcr-1 and which carry this gene on plasmids that are virtually identical to previously described mcr-1–bearing plasmids from Asia and the Middle East. Multiple importations of resistant isolates into the community microflora are to be expected, and these 2 case-patients in Australia had no history of travel outside Australia or direct links to each other. Australia’s regional neighbors use colistin extensively in agriculture (13), but in Australia, its usage in agriculture and healthcare is minimal, and neither colistin nor polymyxin drugs appear in the top 20 antimicrobial drugs prescribed in Australia (14). Notwithstanding the limitations of this opportunistic study, our findings indicate that colistin resistance is unusual among Enterobacteriaceae in Australia and that mcr-1 is neither a key mechanism nor yet widely disseminated in this country despite multiple importation events.

Mr. Ellem is a hospital scientist in the General Microbiology Unit of the Centre for Infectious Diseases and Microbiology Laboratory Services, Westmead Hospital, New South Wales Health Pathology. His research interests are diagnostic methods for rapidly identifying bacterial pathogens and antibiotic resistance in gram-negative bacteria.



We thank Alberto Quesada Molina for providing the control isolate for mcr-1 testing.

A.N.G and J.R.I. were supported in part by the National Health and Medical Research Council of Australia (grants G1046886 and PF1002076, respectively).



  1. Liu  YY, Wang  Y, Walsh  TR, Yi  LX, Zhang  R, Spencer  J, 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. 2016;16:1618. DOIPubMedGoogle Scholar
  2. Snesrud  E, He  S, Chandler  M, Dekker  JP, Hickman  AB, McGann  P, et al. A model for transposition of the colistin resistance gene mcr-1 by ISApl1. Antimicrob Agents Chemother. 2016;60:69736. DOIPubMedGoogle Scholar
  3. Schwarz  S, Johnson  AP. Transferable resistance to colistin: a new but old threat. J Antimicrob Chemother. 2016;71:206670. DOIPubMedGoogle Scholar
  4. Valenzuela  JK, Thomas  L, Partridge  SR, van der Reijden  T, Dijkshoorn  L, Iredell  J. Horizontal gene transfer in a polyclonal outbreak of carbapenem-resistant Acinetobacter baumannii. J Clin Microbiol. 2007;45:45360. DOIPubMedGoogle Scholar
  5. Yao  X, Doi  Y, Zeng  L, Lv  L, Liu  JH. Carbapenem-resistant and colistin-resistant Escherichia coli co-producing NDM-9 and MCR-1. Lancet Infect Dis. 2016;16:2889. DOIPubMedGoogle Scholar
  6. Olaitan  AO, Thongmalayvong  B, Akkhavong  K, Somphavong  S, Paboriboune  P, Khounsy  S, et al. Clonal transmission of a colistin-resistant Escherichia coli from a domesticated pig to a human in Laos. J Antimicrob Chemother. 2015;70:34024.PubMedGoogle Scholar
  7. Zhang  XF, Doi  Y, Huang  X, Li  HY, Zhong  LL, Zeng  KJ, et al. Possible transmission of mcr-1–harboring Escherichia coli between companion animals and human. Emerg Infect Dis. 2016;22:167981. DOIPubMedGoogle Scholar
  8. Brouwer  MS, Tagg  KA, Mevius  DJ, Iredell  JR, Bossers  A, Smith  HE, et al. IncI shufflons: Assembly issues in the next-generation sequencing era. Plasmid. 2015;80:1117. DOIPubMedGoogle Scholar
  9. Suzuki  S, Ohnishi  M, Kawanishi  M, Akiba  M, Kuroda  M. Investigation of a plasmid genome database for colistin-resistance gene mcr-1. Lancet Infect Dis. 2016;16:2845. DOIPubMedGoogle Scholar
  10. Yang  YQ, Li  YX, Song  T, Yang  YX, Jiang  W, Zhang  AY, et al. Colistin resistance gene mcr-1 and its variant in Escherichia coli isolates from chickens in China. Antimicrob Agents Chemother. 2017;61:e0120161. DOIPubMedGoogle Scholar
  11. Poirel  L, Kieffer  N, Brink  A, Coetze  J, Jayol  A, Nordmann  P. Genetic features of MCR-1–producing colistin-resistant Escherichia coli isolates in South Africa. Antimicrob Agents Chemother. 2016;60:43947. DOIPubMedGoogle Scholar
  12. Olaitan  AO, Morand  S, Rolain  JM. Mechanisms of polymyxin resistance: acquired and intrinsic resistance in bacteria. Front Microbiol. 2014;5:643. DOIPubMedGoogle Scholar
  13. Nguyen  NT, Nguyen  HM, Nguyen  CV, Nguyen  TV, Nguyen  MT, Thai  HQ, et al. Use of colistin and other critical antimicrobials on pig and chicken farms in southern Vietnam and its association with resistance in commensal Escherichia coli bacteria. Appl Environ Microbiol. 2016;82:372735. DOIPubMedGoogle Scholar
  14. Australian Commission on Safety and Quality in Health Care. AURA 2016: first Australian report on antimicrobial use and resistance in human health. Sydney: the Commission; 2016.




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DOI: 10.3201/eid2307.161638

Table of Contents – Volume 23, Number 7—July 2017

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Jonathan R. Iredell, CIDM, Level 3, ICPMR Bldg, Westmead Hospital, Westmead, NSW 2145, Australia

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Page created: June 19, 2017
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