Genomic Characteristics of Extended Spectrum β-Lactamase Producing Escherichia coli Isolates Recovered from a District Hospital in China

Characteristics and spatiotemporal changes in phenotypes and genotypes of extended-spectrum β-lactamases in Escherichia coli isolated from bloodstream infections in China from 2014 to 2021

OBJECTIVE

To examine the characteristics and spatiotemporal changes in the phenotypes and genotypes of extended-spectrum β-lactamases (ESBLs) in Escherichia coli strains isolated from bloodstream infections (BSIs) across China between 2014 and 2021.

METHODS

983 ESBL-positive E. coli strains were collected from BSIs in 66 hospitals across different geographic regions in China from 2014 to 2021. The phenotypic confirmation of ESBL was performed through the double-disc diffusion method. The genetic type was determined using polymerase chain reaction (PCR) followed by DNA sequencing.

RESULTS

Between 2014 and 2021, the prevalence of ESBL-positive E. coli steadily decreased from 61.2 to 49.6%. Among 983 phenotypically confirmed ESBL-positive E. coli, 763 (77.6%) were confirmed to carry ESBL genes, with the majority being of the CTX-M type, which is further divided into 23 subtypes and dominated by the CTX-M-9 and CTX-M-1 groups, with 457/763 and 333/763, respectively. Other ESBLs and ampC genes, such as blaOXA-1, blaCMY, and blaDHA-1, often coexisted with either the CTX-M-9 or CTX-M-1 groups. blaCTX-M-14 (34.3%, 157/457) and blaCTX-M-55 (45.9%, 153/333) were the dominant subtypes in the CTX-M-9 and CTX-M-1 groups, respectively. A notable increase in blaCTX-M-27 was observed, particularly from 2019 to 2021, with 26.4%, 23.1%, and 25.8% in all genotypes. Regarding the geographical distribution of the ESBLs, the highest rate of ESBL genetic positivity was observed in Southwest China, accounting for 84.9% (45/53), and the lowest was observed in Northeast China, with 73.2% (30/41). The abundance of the blaCTX-M-27 genotype, in particular, exhibited a notable increase in Southwest China, with 31.4% (14/45) of the strains exhibiting this genotype, followed by the CTX-M-55 genotype, with 13.6% (6/45) of the strains exhibiting this genotype.

CONCLUSIONS

This study demonstrated a steadily decreasing trend in the incidence of ESBLs and predominant CTX-M type ESBLs, particularly the CTX-M-9 and CTX-M-1 groups, in E. coli strains across China, a notable increase in the blaCTX-M-27 genotype and regional variations in the ESBL gene distribution were detected.

Discerning the dissemination mechanisms of antibiotic resistance genes through whole genome sequencing of extended-spectrum beta-lactamase (ESBL)-producing E. coli isolated from veterinary clinics and farms in South Korea

Extended-spectrum beta-lactamase (ESBL)-producing bacteria are resistant to most beta-lactams, including third-generation cephalosporins, limiting the treatment methods against the infections they cause. In this study, we performed whole genome sequencing of ESBL-producing E. coli to determine the mechanisms underlying the dissemination of antibiotic resistance genes. We analyzed 141 ESBL-producing isolates which had been collected from 16 veterinary clinics and 16 farms in South Korea. Long- and short-read sequencing platforms were used to obtain high-quality assemblies. The results showed that blaCTX-M is the dominant ESBL gene type found in South Korea. The spread of blaCTX-M appears to have been facilitated by both clonal spread between different host species and conjugation. Most blaCTX-M genes were found associated with diverse mobile genetic elements that may contribute to the chromosomal integration of the genes. Diverse incompatibility groups of blaCTX-M-harboring plasmids were also observed, which allows their spread among a variety of bacteria. Comprehensive whole genome sequence analysis was useful for the identification of the most prevalent types of ESBL genes and their dissemination mechanisms. The results of this study suggest that the propagation of ESBL genes can occur through clonal spread and plasmid-mediated dissemination, and that suitable action plans should be developed to prevent further propagation of these genes.

Current epidemiologic features and health dynamics of ESBL-producing Escherichia coli in China

Extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (E. coli) are widespread in China, with occurrences documented in humans, animals, and the environment. The dissemination of ESBL-producing E. coli is likely facilitated by the widespread use of antibiotics in human and animal agriculture, the presence of antibiotic-resistant bacteria (ARBs) in animal feces, and close human-animal interactions. Plasmids, particularly those belonging to incompatibility (Inc) group, such as IncF, IncI, and IncH families, play a vital role in facilitating the horizontal gene transfer of ESBL genes across various sectors, from humans to animals and the environment. IS26 and IS1 elements also significantly influences the mobilization and evolution of antibiotic-resistance genes (ARGs), contributing to the spread of ESBL-producing E. coli. bla CTX-M-14, bla CTX-15, and bla CTX-M-55 are prevalent in ESBL-producing E. coli across the three domains and are often found in conjunction with other ARGs. Considering these challenges, it is imperative to take proactive measures to prevent the further spread of ARBs. This includes the judicious and responsible use of antibiotics and efforts to minimize contact with animal feces. Sector-specific strategies should be developed to effectively educate and engage relevant personnel in tackling this multifaceted problem. These efforts are vital to combat the dissemination of ESBL-producing E. coli and preserve public health.