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Emergence of colistin-resistant Escherichia coli clinical isolates harboring mcr-1 in Vietnam

Open AccessPublished:July 10, 2017DOI:https://doi.org/10.1016/j.ijid.2017.07.003

      Highlights

      • Two colistin-resistant Escherichia coli isolates harboring mcr-1 were isolated in a medical setting in Vietnam.
      • The 2 isolates belonged to ST410 and ST457, respectively, and several reports have described the isolation of E. coli ST410 and ST457 from food and pet animals in various countries around the world.
      • The 2 isolates possessed a single copy of an insertion element ISApl1 upstream of mcr-1, which also can contribute to the insertion of mcr-1 from bacterial plasmids into chromosomes.
      • To our knowledge, this is the first report of hospital-acquired E. coli isolates harboring mcr-1 in a medical setting in Vietnam.

      Abstract

      The mcr-1 was first detected on a plasmid in colistin-resistant Escherichia coli from livestock and patients in China. We described here the emergence of colistin-resistant E. coli clinical isolates harboring mcr-1 on the chromosomes in Vietnam. To our knowledge, this is the first report of hospital-acquired E. coli isolates harboring mcr-1 in a medical setting in Vietnam.

      Keywords

      The mcr-1 gene was first reported to be a plasmid-encoded colistin resistance gene in Escherichia coli isolates from food animals and patients in China (
      • Liu Y.Y.
      • Wang Y.
      • Walsh T.R.
      • Yi L.X.
      • 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.
      ). Subsequently, mcr-1-positive strains have been found worldwide in several species of Enterobacteriaceae (
      • Poirel L.
      • Jayol A.
      • Nordmann P.
      Polymyxins: antibacterial activity, susceptibility testing, and resistance mechanisms encoded by plasmids or chromosomes.
      ). This report describes two colistin-resistant E. coli clinical isolates from Vietnam harboring chromosomal mcr-1.
      A total of 18 multidrug-resistant E. coli isolates were obtained in a routine screening of multi-drug resistant Gram-negative pathogens, defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST) (
      • Magiorakos A.P.
      • Srinivasan A.
      • Carey R.B.
      • Carmeli Y.
      • Falagas M.E.
      • Giske C.G.
      • et al.
      Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance.
      ), from March to December 2014 in a hospital in Vietnam. Of them, 2 isolates were resistant to colistin. E. coli strains NCGM-EC88 and NCGM-EC89 were isolated from pus and urine samples of two inpatients in 2014. MICs of various antibiotics were determined using the microdilution method, according to the guidelines of the Clinical Laboratory Standards Institute (
      • Clinical and Laboratory Standards Institute
      Performance standards for antimicrobial susceptibility testing; 25th informational supplement. CLSI M100-S25. Clinical and Laboratory Standards Institute, Wayne, PA.
      ). DNAs were extracted from the isolates using DNeasy Blood & Tissue kits (QIAGEN, Tokyo, Japan) and the entire genomes were sequenced by MiSeq (Illumina, San Diego, CA) and analysed using CLC genomics workbench version 8.0 (CLC bio, Tokyo, Japan). Multilocus sequence typing (MLST) was performed using the MLST database (http://mlst.warwick.ac.uk/mlst/dbs/Ecoli). Pulsed-field gel electrophoresis (PFGE) and Southern hybridization were performed to determine whether mcr-1 was located on plasmids or chromosomes, as previously described (
      • Shrestha B.
      • Tada T.
      • Miyoshi-Akiyama T.
      • Shimada K.
      • Ohara H.
      • Kirikae T.
      • et al.
      Identification of a novel NDM variant, NDM-13, from a multidrug-resistant Escherichia coli clinical isolate in Nepal.
      ). A probe for mcr-1 was amplified by PCR using the primer sets as previously described (
      • Liu Y.Y.
      • Wang Y.
      • Walsh T.R.
      • Yi L.X.
      • 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.
      ).
      As shown in Table 1, the MICs of antibiotics for E. coli strains NCGM-EC88 and NCGM-EC89 showed that both isolates were resistant to ciprofloxacin and colistin, and that NCGM-EC-89 was also resistant to aminoglycosides, whereas both isolates were susceptible to carbapenems. The MICs of colistin for NCGM-EC88 and NCGM-EC89 were 4 and 4 mg/L, respectively. Both isolates harbored mcr-1. NCGM-EC88 harbored aac(3)-IId, aph(3′)-Ia and blaCMY-2; and NCGM-EC89 harbored rmtB, aph(3′)-IIa, blaCTX-M-55, and their MLSTs were ST410 and ST457, respectively.
      Table 1MICs of various antibiotics for E. coli NCGM-EC88 and NCGM-EC89.
      AntibioticsMICs (μg/ml)
      NCGM-EC88NCGM-EC89
      Amikacin21,024
      Arbekacin≤0.5>1,024
      Ciprofloxacin3216
      Colistin44
      Imipenem≤0.5≤0.5
      Meropenem≤0.5≤0.5
      PFGE, Southern blotting and hybridisation analyses revealed that mcr-1 was located on the chromosomes of both NCGM-EC88 and NCGM-89. The genomic environments surrounding mcr-1 in both isolates are shown in Figure 1. The genomic environment surrounding mcr-1 in NCGM-EC88 (nt 5 to nt 3,249; GenBank accession no. LC193130) had a nucleotide sequence 99.6% identical to those in eight E. coli isolates, including six from food animals and two from humans. Of the six isolates from food animals, three, JS-B60 (GenBank accession no. KX254341), 59 (GenBank accession no. KX084394) and SHP45 (GenBank accession no. KU341381), were from the feces of pigs in China; EC2 (GenBank accession no. CP016184) was from the feces of a pig in Malaysia; S38 (GenBank accession no. KX129782) was from poultry meat in Switzerland, and RL465 (GenBank accession no. LT594504) was from a pig in Germany. Of the two isolates from humans, one, Af23 (GenBank accession no. KX032519), was from human blood in South Africa, and the second, ABC149 (GenBank accession no. KX013538), was from human blood in the United Arab Emirates. In seven of these isolates, mcr-1 was encoded on a plasmid, whereas, in the eighth, mcr-1 was encoded on a chromosome (GenBank accession no. LT594504).
      Figure 1
      Figure 1Genomic environments surrounding mcr-1 in NCGM-EC88 and NCGM-EC89.
      The genomic environment surrounding mcr-1 in NCGM-EC89 (nt 1 to nt 11,853; GenBank accession no. LC193131) had a nucleotide sequence 99.8% identical to those in three E. coli isolates, one from a food animal and two from humans; and to the sequence in one Salmonella enterica isolate, from a food animal. Of the isolates from animals, one E. coli SHP45 (GenBank accession no. KU341381), was from the feces of a pig in China, and the other, Salmonella enterica SC23 (GenBank accession no. KU934209), was from a chicken in China. Of the two isolates from humans, one, E. coli ABC149 (GenBank accession no. KX013538), was from human blood in the United Arab Emirates and the other, E. coli Af23, was from human blood in South Africa (GenBank accession no. KX032519).
      The isolates NCGM-EC88 and NCGM-EC89 possibly come from food animals. These isolates belonged to ST410 and ST457, respectively, and several reports have described the isolation of E. coli ST410 and ST457 from food and pet animals in various countries around the world (
      • Poirel L.
      • Jayol A.
      • Nordmann P.
      Polymyxins: antibacterial activity, susceptibility testing, and resistance mechanisms encoded by plasmids or chromosomes.
      ). Each of these isolates, NCGM-EC88 and NCGM-89, possessed a single copy of an insertion element ISApl1 upstream of mcr-1 (Figure 1), suggesting that ISApl1 could have contributed to the acquisition of mcr-1 by these isolates. Moreover, mcr-1 in Enterobacteriaceae might have been mobilized by a single upstream copy of ISApl1 (
      • Snesrud E.
      • He S.
      • Chandler M.
      • Dekker J.P.
      • Hickman A.B.
      • McGann P.
      • et al.
      A model for transposition of the colistin resistance gene mcr-1 by ISApl1.
      ), which also can contribute to the insertion of mcr-1 from bacterial plasmids into chromosomes in NCGM-EC88 and NCGM-EC89.
      Previously, a community-acquired clinical isolate of Shigella sonnei and animal-related E. coli isolates harboring mcr-1, the latter from food animals, have been reported in Vietnam (
      • Malhotra-Kumar S.
      • Xavier B.B.
      • Das A.J.
      • Lammens C.
      • Hoang H.T.
      • Pham N.T.
      • et al.
      Colistin-resistant Escherichia coli harbouring mcr-1 isolated from food animals in Hanoi, Vietnam.
      ,
      • Pham Thanh D.
      • Thanh Tuyen H.
      • Nguyen Thi Nguyen T.
      • Chung The H.
      • Wick R.R.
      • Thwaites G.E.
      • et al.
      Inducible colistin resistance via a disrupted plasmid-borne mcr-1 gene in a 2008 Vietnamese Shigella sonnei isolate.
      ). To our knowledge, however, this is the first report of hospital-acquired E. coli isolates harboring mcr-1 in a medical setting in Vietnam.

      Acknowledgements

      This study was approved by Bach Mai Hospital institutional review board (Approval No. 38) and the Biosafety Committee at the National Center for Global Health and Medicine. This study was supported by J-GRID, and a grant of the Research Program on Emerging and Re-emerging Infectious Diseases from AMED, and JSPS KAKENHI Grant Number 16K19133.

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