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 language | English |
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Article number | e01356-21 |
Number of pages | 13 |
Journal | Microbiology spectrum |
Volume | 10 |
Issue number | 1 |
DOIs | |
Publication status | Published - 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