Genomic epidemiological analysis of mcr-1-harboring Escherichia coli collected from livestock settings in Vietnam

Abstract

Livestock has been implicated as a reservoir for antimicrobial resistance (AMR) genes that can spread to humans when antimicrobials are used in animals for food production to treat clinical diseases and prevent and control common disease events. In Vietnam, mcr-1-harboring Escherichia coli (MCRPEC) strains have been isolated from humans, animals (chickens, pigs, and dogs) feces, flies, foods, and the environment (rainwater, well water, and irrigation water) in communities and from clinical specimens in hospitals. The relationship between levels of AMR in livestock and its occurrence in humans is complex and is driven by many factors. We conducted whole genome sequencing of MCRPEC to analyze the molecular epidemiological characteristics, history, and relatedness of 50 isolates obtained in 2019 from different reservoirs in farms and markets in Ha Nam province, Vietnam. 34 sequence types (STs) with 3 new STs were identified in multilocus sequence typing analysis: ST12945 and ST12946 from chicken feces, and ST12947 from flies. The AMR phenotypes of 50 MCRPEC isolates were as follows: ampicillin (100%, 50/50), cefotaxime (10%, 5/50), gentamicin (60%, 30/50), amikacin (8%, 4/50), meropenem (6%, 3/50), ceftazidime (18%, 9/50), colistin (24%, 12/50) and ciprofloxacin (80%, 40/50). All 50 MCRPEC isolates were identified as MDR. 100% (50/50) isolates carried AMR genes, ranging from 5 to 22 genes. The most prevalent plasmid replicon types carrying mcr-1 were IncP-1 (17/37, 45.9%), IncX4 (7/37, 18.9%), and IncHI2/IncHI2A (6/37, 16.2%). These data suggest that the epidemiology of the mcr-1 gene is mostly determined by plasmid spreading instead of clonal dissemination of MCRPE strains. The co-occurrence of several STs such as ST10, ST48, ST155, ST206, ST2705 in various sample types, joined to the higher prevalence of a few types of Inc plasmids, confirms the dissemination of the mcr-1 carrying plasmids in E. coli clones established in livestock. 5 over 8 STs identified in flies (ST206, ST2705, ST155, ST10, and ST48) suggested the fly contribution in the transmission of AMR bacteria in environments. These popular STs also occur in human samples and 100% of the human samples were positive for the mcr-1 gene.

Epidemiological and genomic characteristics of global mcr-positive Escherichia coli isolates

“…The high incidence of mcr in our study is in accordance with a previous report ( Dadashi et al, 2022 ), consistent with its identification as the globally predominant colistin-resistance gene. At present, mcr -1 could confer colistin resistance with broad minimal inhibitory concentrations (MICs) of 2–16 mg/L ( Nang et al, 2019 ), for instance, 74% of mcr -1 positive E. coli isolates had MICs at 2 mg/L ( Nguyen et al, 2022 ), while 52% of mcr -1 positive E. coli isolates in another study exhibited MICs of 4∼8 mg/L ( Ćwiek et al, 2021 ). For other mcr genes, mcr -3 has been globally disseminated since it was first reported in Yin et al (2017) , and this gene inside the linker has been found to appear as a facilitator of colistin resistance ( Xu et al, 2021 ).…”

Integration of water, sanitation, and hygiene program with biosecurity: A One Health approach to reduce the prevalence and exposure of antibiotic-resistant bacteria in the livestock community

“…The prevalence of multidrug-resistant (MDR) E. coli has been observed in Asia [49][50][51][52][53][54], Africa [55][56][57][58], and four European countries [59], with varied rates and resistance to more than four types of medicines. Further research is required to understand the transmission mechanism of MDR E. coli within agricultural contexts and the risk variables that affect temporal changes.…”

Comparative genome analysis of colistin-resistant Escherichia coli harboring mcr isolated from rural community residents in Ecuador and Vietnam

“…Due to the high prevalence of colistin-resistant E . coli carrying mcr in livestock as well as the possibility of horizontal transfer among various hosts, there is a high risk of the spread of resistant bacteria in the human community, given that animals are used for food production [ 17 ]. Such a spread among communities and regions may be influenced by the people’s lifestyles, which may also affect colistin-resistant bacteria epidemic patterns.…”