Genomic Comparison Reveals Natural Occurrence of Clinically Relevant Multidrug-Resistant Extended-Spectrum-β-Lactamase-Producing Escherichia coli Strains

Abstract

The effectiveness of antibiotics has been challenged by the increasing frequency of antimicrobial resistance (AMR), which has emerged as a major threat to global health. Despite its negative impact on the development of AMR, there are few effective strategies for reducing AMR in food-producing animals. Using wholegenome sequencing and comparative genomics of 36 multidrug-resistant (MDR) Escherichia coli strains isolated from beef cattle with no previous exposure to antibiotics, we obtained results suggesting that the occurrence of MDR E. coli also arises in animals with no antibiotic selective pressure. Extended-spectrum-␤-lactamaseproducing E. coli strains with enhanced virulence capacities for toxin production and adherence have evolved, which implies important ramifications for animal and human health. Gene exchanges by conjugative plasmids and insertion elements have driven widespread antibiotic resistance in clinically relevant pathogens. Phylogenetic relatedness of E. coli strains from various geographic locations and hosts, such as animals, environmental sources, and humans, suggests that transmission of MDR E. coli strains occurs intercontinentally without host barriers. IMPORTANCE Multidrug-resistant (MDR) Escherichia coli isolates pose global threats to public health due to the decreasing availability of treatment options. To better understand the characteristics of MDR E. coli isolated from food-producing animals with no antibiotic exposure, we employed genomic comparison, high-resolution phylogenetics, and functional characterization. Our findings highlight the potential capacity of MDR E. coli to cause severe disease and suggest that these strains are widespread intercontinentally. This study underlines the occurrence of MDR E. coli in food-producing animals raised without antibiotic use, which has alarming, critical ramifications within animal and human medical practice.

Panoramic Insights into the Microevolution and Macroevolution ofPrevotella copri-containing Lineage in Primate Guts

“…Poor host and geographical barrier have been observed in animal-associated microbial transmission (21,47,56,57). Non-strict biogeographic distribution for subspecies-level profile of P. copri in human gut was proven by our study as well as by Tett et al (30).…”

Prevalence and Molecular Characteristics of Extended-Spectrum and AmpC β-Lactamase Producing Escherichia coli in Grazing Beef Cattle

“…As potential routes, antibiotic resistant bacteria can be transferred to animals through the environment, without the exposure of antibiotics before (Mir et al, 2016(Mir et al, , 2018Teng et al, 2019). To understand whether farm environment could be outside sources of antibiotic resistant bacteria in animals, and to identify which environmental factors are mostly critical to the animals, the prevalence and concentration of CTX-M and CMY-2 positive isolates were compared based on the sample types.…”

Prevalence of extended-spectrum β-lactamases in the local farm environment and livestock: challenges to mitigate antimicrobial resistance

“…Not surprisingly, isolates defined as the same strains by low-resolution techniques were found to be non-clonal variants (Knudsen et al 2017;Guo et al 2018). In our recent study (Teng et al 2019), strains belonging to the same ST with an identical profile of virulence genes did not cluster together in a phylogenetic tree. To overcome the issues raised by low-resolution techniques, the GenomeTrakr network has been created by the Food and Drug Administration (FDA) to track pathogens that caused foodborne outbreaks, by comparing variant SNPs in the whole genomes of the isolated strains (Wang et al 2016).…”

“…Cattle raised in cow/calf operation systems on pasture with limited use of antibiotics to occasional treatment carried CRB, although the prevalence was relatively low, 47.4%, compared to the prevalence of CRB in feedlot (83%) (Noyes et al 2016;Markland et al 2019). Furthermore, genetically similar ESBL-producing E. coli have been isolated in various hosts around the world (Teng et al 2019). These observations suggest that AR in livestock can arise through various environmental pathways, even in the absence of anthropogenic antibiotic use Mir et al 2016).…”

“…A prototype of CTX-M type ESBLs has been found to originate from environmental bacteria Kluyvera species (Bevan et al 2017). Most ESBL-producing bacteria encode the ESBL genes on plasmids facilitating the rapid spread through horizontal gene transfer (HGT) between bacteria, but recent findings indicate that the bla CTX-M genes are also encoded in chromosomal DNA (Teng et al 2019).…”