Characterization of Genetic Elements Carrying mcr-1 Gene in Escherichia coli from the Community and Hospital Settings in Vietnam

Bich Vu Thi Ngoc*, Thanh Le Viet, Mai Nguyen Thi Tuyet, Thuong Nguyen Thi Hong, Diep Nguyen Thi Ngoc, Duyet Le Van, Loan Chu Thi, Hoang Tran Huy, John Penders, Heiman Wertheim, H Rogier van Doorn

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

Abstract

Colistin is widely used in agriculture and aquaculture as prophylaxis, particularly in Asia. Recently, mcr-1 and other mobilizable genes conferring colistin resistance have spread globally in community and hospital populations. Characterizing mcr-1 mobile genetic elements and host genetic background is important to understand the transmission of this resistance mechanism. We conducted whole-genome sequencing of 94 mcr-1-positive Escherichia coli isolates (Mcr1-Ec isolates) from human and animal feces, food, and water in a community cohort (N = 87) and from clinical specimens from a referral hospital (N = 7) in northern Vietnam. mcr-1 was plasmid-borne in 71 and chromosomally carried in 25 (2 isolates contain one copy on chromosome and one copy on a plasmid) of 94 E. coli isolates from the community and hospital settings. All seven clinical isolates carried mcr-1 on plasmids. Replicon types of mcr-1-carrying plasmids included IncI2, IncP, IncX4, and IncFIA single replicons and combinations of IncHI2, IncN, and IncX1 multireplicons. Alignment of a long-read sequence of an IncI2 plasmid from animal feces with short-read sequences of IncI2 plasmids from a healthy human, water, and hospitalized patients showed highly similar structures (query cover from 90% to 98%, overall identity of >81%). We detected the potential existence of multireplicon plasmids harboring mcr-1 regardless of sample setting, confirming 10/71 with long-read sequencing. An intact/conserved Tn6330 transposon sequence or its genetic context variants were found in 6/25 Mcr1-Ec isolates with chromosomally carried mcr-1. The dissemination of mcr-1 is facilitated by a high diversity of plasmid replicon types and a high prevalence of the chromosomal Tn6330 transposon. IMPORTANCE The article presented advances our understanding of genetic elements carrying mcr-1 in Escherichia coli in both community and hospital settings. We provide evidence to suggest that diverse plasmid types, including multireplicon plasmids, have facilitated the successful transmission of mcr-1 in different reservoirs. The widespread use of colistin in agriculture, where a high diversity of bacteria are exposed, has allowed the selection and evolution of various transmission mechanisms that will make it a challenge to get rid of. Colocalization of mcr-1 and other antibiotic resistance genes (ARGs) on multireplicon plasmids adds another layer of complexity to the rapid dissemination of mcr-1 genes among community and hospital bacterial populations and to the slow pandemic of antimicrobial resistance (AMR) in general.

Original languageEnglish
Article numbere01356-21
Number of pages13
JournalMicrobiology spectrum
Volume10
Issue number1
DOIs
Publication statusPublished - 23 Feb 2022

Keywords

  • Anti-Bacterial Agents/pharmacology
  • Colistin/pharmacology
  • Drug Resistance, Bacterial
  • Escherichia coli Infections/microbiology
  • Escherichia coli Proteins/genetics
  • Escherichia coli/classification
  • Feces/microbiology
  • Hospitals/statistics & numerical data
  • Humans
  • Interspersed Repetitive Sequences
  • Microbial Sensitivity Tests
  • Phylogeny
  • Plasmids/genetics
  • Vietnam
  • PLASMIDS
  • multireplicon plasmid
  • Escherichia coli
  • ALGORITHM
  • plasmid harboring mcr-1
  • One health
  • antimicrobial resistance
  • ANNOTATION
  • mcr-1 transmission
  • CARBAPENEMASE
  • REPLICON
  • RESISTANCE
  • colistin resistance
  • KLEBSIELLA-PNEUMONIAE

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