Comparison of antimicrobial resistance and molecular characterization of Escherichia coli isolates from layer breeder farms in Korea

Whole-genome sequence-based comparison of antimicrobial resistant diarrheagenic Escherichia coli in pork and chicken production chains in Korea

Diarrheagenic Escherichia coli (DEC) is a serious public health threat. We investigated the distribution, antimicrobial resistance, and molecular characteristics of DEC in pork and chicken production chains following the "One Health" approach. We collected 1567 pig- and 771 chicken-associated samples from animal farms, slaughterhouses, and retail markets. Of these samples, we identified 150 DEC isolates, with 73 (4.7 %) originating from pigs and 77 (10 %) from chickens. DEC risk of contamination in the final product (meat) was significantly higher in chickens (27.3 %) compared to pigs (0.5 %). In addition, carryover meat contamination was observed by clones originating from slaughterhouses in the chicken meat production chain. The resistance of chicken-associated isolates compared to pig-associated isolates to most antimicrobial agents was higher. Phylogenetic analysis following whole-genome sequencing of 150 DEC showed distinct lineages based on the host species, resulting in 20 clusters and 16 singletons. Multilocus sequence typing and serotyping revealed 25 and 30 different sequence types (STs) and serotypes, respectively. Human infection-related STs, including ST10 (11 %), ST23 (2.3 %), and ST48 (6.8 %), along with serotypes O89 (12.3 %), O26 (6.8 %), O103 (5.5 %), O121 (2.7 %), and O145 (2.7 %), were commonly detected in pig-associated isolates, emphasizing a zoonotic risk. Furthermore, the presence of various plasmids containing antimicrobial resistance and virulence genes was evident, posing a risk of spreading these genes to clinically important pathogens. Therefore, implementing effective control programs to reduce the prevalence of antimicrobial-resistant DEC in food production systems is important.

Multidrug-Resistant Escherichia coli in Broiler and Indigenous Farm Environments in Klang Valley, Malaysia

Background/Objectives: The global health threat posed by antimicrobial resistance (AMR) is a cause for serious concern. Poultry farming in Asia, particularly with indiscriminate use, has been identified as a major contributor to AMR, resulting in the emergence of multidrug-resistant (MDR) bacteria, particularly Escherichia coli (E. coli). Considering the environment's role in harboring pathogens, this study aimed to determine the distribution of MDR E. coli in the environments of broiler and indigenous farms in Klang Valley, Malaysia. Methods: Soil and effluent samples were collected from 30 poultry (19 broiler and 11 indigenous) farms. Selective chromogenic E. coli agar plates were used for the isolation of bacteria. The VITEX® 2 system was employed for identification and susceptibility testing. Results: A total of 117 E. coli isolates were recovered. The isolates were highly resistant to ampicillin (76.1%), followed by trimethoprim-sulfamethoxazole (47.9%), and ampicillin-sulbactam (46.2%). AMR rates were higher in broiler farms (91.3%) than in indigenous farms (64.6%) (p < 0.05). The high multiple antibiotic resistance index in the environment of broiler farms (0.22) implies a higher risk of contamination compared to indigenous farms (0.10). Conclusions: The elevated levels of AMR observed in broiler farms underscore the need for collaborative efforts across sectors to address this issue. As AMR is a global One Health issue, monitoring AMR in the environment is essential to complement existing health programs. Implementing best practices, biosecurity, hygiene, continuous monitoring, and food safety management systems is crucial to reduce antimicrobial use and curb the rise of MDR bacteria.

Antibiotics' resistance profile of pathogens isolated from fish products sold in the city of Bangangté, Cameroon: Aqueous extracts from spices' formulations used as accompanying soup of braised fish as antimicrobial alternative

The present study aimed to evaluate the antimicrobial activity of aqueous extracts of the mixture of spices used as accompanying soup of braised fish against multidrug resistant (MDR) bacteria isolated from raw and braised fish collected in the city of Bangangté, Cameroon. A survey was conducted in the city of Bangangté to diagnose the braising fish processes. Pathogens were isolated from raw and braised fish samples collected in fish farms and selling points, and their susceptibility to 16 commonly used antibiotics was tested using the Kirby-Bauer disk diffusion method. The aqueous extracts of spices' formulations used as accompanying soup of braised fish were tested against MDR isolates using the well diffusion method. The results revealed that 13 spices are used in the preparation of accompanying soups of braised fish. Three formulations were identified with mbongo, clove and prekeses as the main differential spices. These formulations were either heated at 100 °C/30 min (process 1) or not (process 2) before being served to consumers'. Fifty-five strains belonging to six species (Salmonella Typhi, Salmonella Paratyphi, Escherichia coli, Escherichia vulneralis, Staphylococcus aureus and Staphylococcus spp.) were isolated from the different samples. Forty-four isolates were resistant to several antibiotics with Multiple Antibiotic Resistance indexes ranging from 0.18 to 0.81. The aqueous extracts of all the formulations were active against the MDR isolates independent of the formulation and preparation process, with inhibition diameters varying significantly (p < 0.05) from one isolate to another. Heated extracts were less active than the unheated ones and the most active extract was from the formulation including clove. The strains E. coli and E. vulneralis were most resistant to the different extracts whereas S. Typhi, S. aureus, Staphylococcus spp. and S. Paratyphi A, were more sensitive. This study evidenced that fish products from Bangangté city contain MDR pathogens and demonstrated that the formulations of spices used as accompanying soup for braised fish are active against these MDR pathogens. It suggests their potential use as strategy to combat the antimicrobial resistance phenomena associated to foodborne gastroenteritis pathogens. It also suggests that more attention should be paid to the use of antibiotics in fish farming activities.

Molecular epidemiology and transmission of rmtB-positive Escherichia coli among ducks and environment

This study aimed to investigate the transmission and molecular epidemiological characteristics of the rmtB gene in Escherichia coli (E. coli) strains isolated from duck farms in Guangdong Province of China from 2018 to 2021. A total of 164 (19.4%, 164/844) rmtB-positive E. coli strains were recovered from feces, viscera, and environment. We performed antibiotic susceptibility tests, pulsed-field gel electrophoresis (PFGE), and conjugation experiments. We obtained the genetic context of 46 rmtB-carrying E. coli isolates and constructed a phylogenetic tree via whole genome sequencing (WGS) and bioinformatic analysis. The isolation rate of rmtB-carrying E. coli isolates in duck farms increased yearly from 2018 to 2020 but decreased in 2021. All rmtB-harboring E. coli strains were multidrug resistant (MDR), and 99.4% of the strains were resistant to more than 10 drugs. Surprisingly, duck- and environment-associated strains similarly showed high MDR. Conjugation experiments revealed that the rmtB gene horizontally cocarried bla_CTX-M and bla_TEM gene dissemination via IncFII plasmids. Insertion sequences IS26, ISCR1, and ISCR3 were closely associated with the spread of rmtB-harboring E. coli isolates. WGS analysis indicated that ST48 was the most prevalent sequence type. The results of single nucleotide polymorphism (SNP) differences revealed potential clonal transmission between ducks and the environment. Based on One Health principles, we need to strictly use veterinary antibiotics, monitor the distribution of MDR strains, and evaluate the impact of plasmid-mediated rmtB gene on human, animal, and environmental health.

Comparative Analysis of Phylogenetic Relationships and Virulence Factor Characteristics between Extended-Spectrum β-Lactamase-Producing Escherichia coli Isolates Derived from Clinical Sites and Chicken Farms

Antimicrobial resistance in bacteria is the most urgent global threat to public health, with extended-spectrum β-lactamase-producing Escherichia coli (ESBL-E. coli) being one of the most documented examples. Nonetheless, the ESBL-E. coli transmission relationship among clinical sites and chicken farms remains unclear. Here, 408 ESBL-E. coli strains were isolated from hospitals and chicken farms in Sichuan Province and Yunnan Province in 2021. We detected blaCTX-M genes in 337 (82.62%) ESBL-E. coli strains. Although the isolation rate, prevalent sequence type (ST) subtypes, and blaCTX-M gene subtypes of ESBL-E. coli varied based on regions and sources, a few strains of CTX-ESBL-E. coli derived from clinical sites and chicken farms in Sichuan Province displayed high genetic similarity. This indicates a risk of ESBL-E. coli transmission from chickens to humans. Moreover, we found that the high-risk clonal strains ST131 and ST1193 primarily carried blaCTX-M-27. This indicates that drug-resistant E. coli from animal and human sources should be monitored. As well, the overuse of β-lactam antibiotics should be avoided in poultry farms to ensure public health and build an effective regulatory mechanism of "farm to fork" under a One Health perspective. IMPORTANCE Bacterial drug resistance has become one of the most significant threats to human health worldwide, especially for extended-spectrum β-lactamase-producing E. coli (ESBL-E. coli). Timely and accurate epidemiological surveys can provide scientific guidance for the adoption of treatments in different regions and also reduce the formation of drug-resistant bacteria. Our study showed that the subtypes of ESBL-E. coli strains prevalent in different provinces are somewhat different, so it is necessary to individualize treatment regimens in different regions, and it is especially important to limit and reduce antibiotic use in poultry farming since chicken-derived ESBL-E. coli serves as an important reservoir of drug resistance genes and has the potential to spread to humans, thus posing a threat to human health. The use of antibiotics in poultry farming should be particularly limited and reduced.

GLO1 Contributes to the Drug Resistance of Escherichia coli Through Inducing PER Type of Extended-Spectrum β-Lactamases

Background

Escherichia coli-associated antimicrobial resistance (AMR) issue so far needs urgent considerations. This study aims to screen the potent genes associated with extended-spectrum β-lactamases (ESBLs) in drug-resistant Escherichia coli and elucidate the specific drug-resistant mechanism.

Methods

Clinical ESBLs-EC samples were obtained based on the microbial identification, and the whole genome was sequenced. In combination with the significantly enriched pathways, several differently expressed genes were screened and verified by RT-PCR. Furthermore, through knocking out glyoxalase 1 (GLO1) gene and transfecting overexpressed plasmids, the potential relationship between GLO1 and ESBLs was then investigated. Lastly, the concentrations of β-lactamases in bacteria and supernatant from different groups were examined by enzyme-linked immunosorbent assay (ELISA).

Results

After successful isolation and identification of ESBLs-EC, the whole genome and eighteen differential metabolic pathways were analyzed to select differently expressed genes, including add, deoD, guaD, speG, GLO1, VNN1, etc. RT-PCR results showed that there were no differences in these genes between the standard bacteria and susceptible Escherichia coli. Remarkably, the relative levels of four genes including speG, Hdac10, GLO1 and Ppcdc were significantly increased in ESBLs-EC in comparison with susceptible strains, whereas other gene expression was decreased. Further experiments utilizing gene knockout and overexpression strains confirmed the role of GLO1. At last, a total of 10 subtypes of β-lactamases were studied using ELISA, including BES-, CTX-M1-, CTX-M2-, OXA1-, OXA2-, OXA10-, PER-, SHV-, TEM-, and VEB-ESBLs, and results demonstrated that GLO1 gene expression only affected PER-β-lactamases but had no effects on other β-lactamases.

Conclusion

SpeG, Hdac10, GLO1 and Ppcdc might be associated with the drug-resistant mechanism of Escherichia coli. Of note, this study firstly addressed the role of GLO1 in the drug resistance of ESBLs-EC, and this effect may be mediated by increasing PER-β-lactamases.