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

• Published in: Microbiology spectrum Vol. 10; no. 1; p. e0135621
• Main Authors: Vu Thi Ngoc, Bich, Le Viet, Thanh, Nguyen Thi Tuyet, Mai, Nguyen Thi Hong, Thuong, Nguyen Thi Ngoc, Diep, Le Van, Duyet, Chu Thi, Loan, Tran Huy, Hoang, Penders, John, Wertheim, Heiman, van Doorn, H Rogier
• Format: Journal Article
• Language: English
• Published: United States American Society for Microbiology 23.02.2022
• Subjects: Anti-Bacterial Agents - pharmacology; Antimicrobial Chemotherapy; antimicrobial resistance; Colistin - pharmacology; colistin resistance; Drug Resistance, Bacterial; Escherichia coli - classification; Escherichia coli - drug effects; Escherichia coli - genetics; Escherichia coli - metabolism; Escherichia coli Infections - microbiology; Escherichia coli Proteins - genetics; Feces - microbiology; Hospitals - statistics & numerical data; Humans; Interspersed Repetitive Sequences; mcr-1 transmission; Microbial Sensitivity Tests; multireplicon plasmid; One health; Phylogeny; plasmid harboring mcr-1; Plasmids - genetics; Plasmids - metabolism; Research Article; Vietnam; Vietnam; plasmid harboring mcr-1; One health; multireplicon plasmid; mcr-1 transmission; antimicrobial resistance; Escherichia coli; colistin resistance
• ISSN: 2165-0497; 2165-0497
• DOI: 10.1128/spectrum.01356-21

Colistin is widely used in agriculture and aquaculture as prophylaxis, particularly in Asia. Recently, and other mobilizable genes conferring colistin resistance have spread globally in community and hospital populations. Characterizing mobile genetic elements and host genetic background is important to understand the transmission of this resistance mechanism. We conducted whole-genome sequencing of 94 -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. 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 on plasmids. Replicon types of -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 regardless of sample setting, confirming 10/71 with long-read sequencing. An intact/conserved transposon sequence or its genetic context variants were found in 6/25 Mcr1-Ec isolates with chromosomally carried . The dissemination of is facilitated by a high diversity of plasmid replicon types and a high prevalence of the chromosomal transposon. The article presented advances our understanding of genetic elements carrying 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 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 and other antibiotic resistance genes (ARGs) on multireplicon plasmids adds another layer of complexity to the rapid dissemination of genes among community and hospital bacterial populations and to the slow pandemic of antimicrobial resistance (AMR) in general.