Comparative Characteristics and Pathogenic Potential of Escherichia coli Isolates Originating from Poultry Farms, Retail Meat, and Human Urinary Tract Infection

Antimicrobial Resistance in the Context of Animal Production and Meat Products in Poland-A Critical Review and Future Perspective

The prevalence of antimicrobial-resistant bacteria in meat and meat products is a significant public health challenge, largely driven by the excessive and inappropriate use of antimicrobials in animal husbandry. In Poland, a key meat producer in Europe, antibiotic-resistant pathogens such as Campylobacter spp., Staphylococcus spp., Enterococcus spp., Listeria monocytogenes, and Enterobacterales have been detected in meat, posing serious risks to consumers. This review examines the use of antimicrobial agents in meat production and the resulting antimicrobial resistance (AMR) in microorganisms isolated from meat products in Poland. The mechanisms of AMR, genetic factors, and prevalence in Poland are presented. It highlights key factors contributing to AMR, such as antibiotic misuse in livestock farming, and discusses the legal regulations governing veterinary drug residues in food. This review emphasizes the importance of monitoring and enforcement to safeguard public health and calls for further research on AMR in the meat industry. Antimicrobial resistance in meat and meat products in Poland is a huge challenge, requiring stricter antibiotic controls in animal husbandry and improved surveillance systems. Additionally, the impact of husbandry practices on the environment and food requires further research. Future efforts should focus on nationwide monitoring, alternative strategies to reduce antibiotic use, and stronger enforcement to combat antimicrobial resistance and protect public health.

Draft genome sequence of a co-harbouring blaNDM-5 and mcr-1.1 Escherichia coli phylogroup A isolate associated with patient colonisation in Ireland

OBJECTIVES

While Escherichia coli phylogroup-A is typically associated with commensal strains, some isolates can harbour virulence and exhibit multidrug-resistant (MDR) phenotypes. We report the draft genome of a rare instance of carbapenem, fosfomycin and colistin resistant E. coli phylogroup-A, isolated as part of routine screening of a human patient in a clinical setting in Ireland.

METHODS

E. coli E230738 was identified using MALDI-ToF/MS. Antibiotic susceptibility testing was performed using the Sensititre-EUMDRXXF plate. Whole-genome-sequencing was conducted with NextSeq1000, and genomic analysis identified antibiotic-resistance-genes (ARGs) and virulence-factors (VFs). Phylogenetic analysis was performed using whole-genome-multilocus-sequence-typing (wgMLST).

RESULTS

E. coli E230738 genome was identified to belong to phylogroup-A/ST10 complex and to harbour 63 ARGs, 17 of which acquired. Resistance to beta-lactams, including carbapenems and cephalosporins was likely due to chromosomally identified blaNDM-5. Colistin resistance appeared associated with acquired mcr-1.1. Despite lacking fosfomycin-inactivating-enzymes, fosfomycin resistance was observed, possibly due to efflux pumps. Forty-seven chromosomal VFs were identified, involved in adhesion and iron acquisition amongst other properties. Plasmid replicons associated with the spread of MDR genes such as IncHI2/HI2A were detected. wgMLST analysis showed the closest relative being a strain from the UK, exhibiting differences in the sequences of 851 genes.

CONCLUSION

This is a first detected instance of a blaNDM-5 and mcr-1.1 co-occurring in E. coli in Ireland. The MDR profile of E. coli E230738 highlights the growing public health concern posed by the dissemination of MDR E. coli lineages with limited treatment options and underscores the need for clinical screening coupled with genomic surveillance to better understand evolving MDR patterns in E. coli.

Determining the In Vivo Efficacy of Plant-Based and Probiotic-Based Antibiotic Alternatives against Mixed Infection with Salmonella enterica and Escherichia coli in Domestic Chickens

Restrictions on the use of antimicrobial compounds have led to a surge of interest in alternative solutions, such as natural, plant-based compounds. In our study, we investigated the efficacy of three feed supplements containing different additives, namely, probiotics (Lactobacillus spp., "Test substance A"), turmeric (Curcuma longa L., "Test substance B"), and fenugreek (Trigonella foenum graecum, "Test substance C"). In the experiment, we tested 180 birds of the Bábolna Tetra-SL laying hybrid breed that were infected with Salmonella enteritidis strains. The birds were randomly divided into six groups: three groups treated with the different additives, a negative control group, a positive control group, and an antibiotic-treated group using enrofloxacin. We examined the maturation and the time course of shedding of Salmonella; at the end of rearing, pathological and histopathological examinations were performed. When Salmonella was isolated from the cloacal swab samples, the enrofloxacin-treated group had a high number of animals shedding Salmonella by day 9, which was like the group treated with test material C. The greatest reduction in Salmonella shedding was observed in the groups treated with test materials A and B. In terms of pathological parameters, villus length and crypt depth were significantly better in the group treated with test material C compared to the positive and negative controls, and when comparing the body weight of the tested animals, the group treated with test material B had a significantly larger absorption surface area compared to the positive control group. Overall, the supplement with test material C proved to be the most effective. In the future, it is worthwhile to investigate the combination of the tested active substances for their possible synergistic effects and to perform a dose-response study to select the optimal dosage.

Comprehensive probiogenomics analysis of the commensal Escherichia coli CEC15 as a potential probiotic strain

BACKGROUND

Probiotics have gained attention for their potential maintaining gut and immune homeostasis. They have been found to confer protection against pathogen colonization, possess immunomodulatory effects, enhance gut barrier functionality, and mitigate inflammation. However, a thorough understanding of the unique mechanisms of effects triggered by individual strains is necessary to optimize their therapeutic efficacy. Probiogenomics, involving high-throughput techniques, can help identify uncharacterized strains and aid in the rational selection of new probiotics. This study evaluates the potential of the Escherichia coli CEC15 strain as a probiotic through in silico, in vitro, and in vivo analyses, comparing it to the well-known probiotic reference E. coli Nissle 1917. Genomic analysis was conducted to identify traits with potential beneficial activity and to assess the safety of each strain (genomic islands, bacteriocin production, antibiotic resistance, production of proteins involved in host homeostasis, and proteins with adhesive properties). In vitro studies assessed survival in gastrointestinal simulated conditions and adhesion to cultured human intestinal cells. Safety was evaluated in BALB/c mice, monitoring the impact of E. coli consumption on clinical signs, intestinal architecture, intestinal permeability, and fecal microbiota. Additionally, the protective effects of both strains were assessed in a murine model of 5-FU-induced mucositis.

RESULTS

CEC15 mitigates inflammation, reinforces intestinal barrier, and modulates intestinal microbiota. In silico analysis revealed fewer pathogenicity-related traits in CEC15, when compared to Nissle 1917, with fewer toxin-associated genes and no gene suggesting the production of colibactin (a genotoxic agent). Most predicted antibiotic-resistance genes were neither associated with actual resistance, nor with transposable elements. The genome of CEC15 strain encodes proteins related to stress tolerance and to adhesion, in line with its better survival during digestion and higher adhesion to intestinal cells, when compared to Nissle 1917. Moreover, CEC15 exhibited beneficial effects on mice and their intestinal microbiota, both in healthy animals and against 5FU-induced intestinal mucositis.

CONCLUSIONS

These findings suggest that the CEC15 strain holds promise as a probiotic, as it could modulate the intestinal microbiota, providing immunomodulatory and anti-inflammatory effects, and reinforcing the intestinal barrier. These findings may have implications for the treatment of gastrointestinal disorders, particularly some forms of diarrhea.

Antimicrobial-Resistant Escherichia coli, Enterobacter cloacae, Enterococcus faecium, and Salmonella Kentucky Harboring Aminoglycoside and Beta-Lactam Resistance Genes in Raw Meat-Based Dog Diets, USA

The practice of feeding raw meat-based diets to dogs has grown in popularity worldwide in recent years. However, there are public health risks in handling and feeding raw meat-based dog diets (RMDDs) to dogs since there are no pathogen reduction steps to reduce the microbial load, which may include antimicrobial-resistant pathogenic bacteria. A total of 100 RMDDs from 63 suppliers were sampled, and selective media were used to isolate bacteria from the diets. Bacterial identification, antimicrobial susceptibility testing, and whole-genome sequencing (WGS) were conducted to identify antimicrobial resistance (AMR). The primary meat sources for RMDDs included in this study were poultry (37%) and beef (24%). Frozen-dry was the main method of product production (68%). In total, 52 true and opportunistic pathogens, including Enterobacterales (mainly Escherichia coli, Enterobacter cloacae) and Enterococcus faecium, were obtained from 30 RMDDs. Resistance was identified to 19 of 28 antimicrobials tested, including amoxicillin/clavulanic acid (23/52, 44%), ampicillin (19/52, 37%), cephalexin (16/52, 31%), tetracycline (7/52, 13%), marbofloxacin (7/52, 13%), and cefazolin (6/52, 12%). All 19 bacterial isolates submitted for WGS harbored at least one type of AMR gene. The identified AMR genes were found to mediate resistance to aminoglycoside (gentamicin, streptomycin, amikacin/kanamycin, gentamicin/kanamycin/tobramycin), macrolide, beta-lactam (carbapenem, cephalosporin), tetracycline, fosfomycin, quinolone, phenicol/quinolone, and sulfonamide. In conclusion, the results of this study suggest that feeding and handling RMDDs may pose a significant public health risk due to the presence of antimicrobial-resistant pathogens, and further research and intervention may be necessary to minimize these risks.

Occurrence of Major Human Extraintestinal Pathogenic Escherichia coli Sequence Types Among Diarrheic Pet Animals: A Potential Public Health Threat

Background: Extraintestinal pathogenic Escherichia coli (ExPEC) has become a mounting public health concern. The present study was conducted to address the role of diarrheic pet animals as potential reservoirs for major human ExPEC sequence types (STs). Materials and Methods: Rectal swabs were collected from 145 diarrheic pet animals (75 dogs and 70 cats). Samples were processed for isolation and identification of E. coli by culture methods. Afterward, ExPEC isolates were identified on a molecular basis through detection of ExPEC phylogroups (B2 and D) coupled with carriage of two or more of the virulence genes associated with ExPEC (papAH, papC, sfa/focDE, afa/draBC, iutA, and kpsMT II). ExPEC STs 131, 73, 69, and 95 were identified among ExPEC isolates by quadruplex PCR and tested for their antimicrobial susceptibility. Eventually, two isolates underwent gene sequencing for the phylogenetic analysis. Results: Of 145 pet animals, 16 (11%) E. coli strains were identified as ExPEC, in which 15 (10.3%) isolates belonged to phylogroup B2 and 1 (0.69%) strain belonged to phylogroup D. The major human ExPEC STs were detected in 13 (9%) isolates, whereas the prevalence rates were 5.3% and 12.9% for dogs and cats, respectively. The isolation rates of ExPEC STs were 4.8%, 2.8%, 0.69%, and 0.69% for ST73, ST131, ST95, and ST69, respectively. Regarding the prevalence of virulence genes among ExPEC STs, the most prevalent ones were papC and sfa/focDE (92.3%), followed by papAH (76.9%), iutA (53.8%), afa/draBC (30.8%), and kpsMT II (30.8%). Moreover, 38.5% of the obtained human ExPEC STs were multidrug resistant. The phylogenetic analysis of two ExPEC ST73 gene sequences showed high genetic relatedness to those isolated from humans in different countries. Conclusions: The fecal carriage of major human ExPEC STs among diarrheic dogs and cats poses a potential zoonotic hazard with serious public health implications.

Exposing Salmonella Senftenberg and Escherichia coli Strains Isolated from Poultry Farms to Formaldehyde and Lingonberry Extract at Low Concentrations

European Union (EU) countries strive to improve the quality and safety of food of animal origin. Food production depends on a good microbiological quality of fodder. However, feed can be a reservoir or vector of pathogenic microorganisms, including Salmonella or Escherichia coli bacteria. Salmonella spp. and E. coli are the two most important food-borne pathogens of public health concern. Contamination with these pathogens, mainly in the poultry sector, can lead to serious food-borne diseases. Both microorganisms can form biofilms on abiotic and biotic surfaces. The cells that form biofilms are less sensitive to disinfectants, which in turn makes it difficult to eliminate them from various surfaces. Because the usage of formaldehyde in animal feed is prohibited in European countries, the replacement of this antibacterial with natural plant products seems very promising. This study aimed to assess the inhibitory effectiveness of Vaccinium vitis-idaea extract against biofilm produced by model Salmonella enterica and E. coli strains. We found that formaldehyde could effectively kill both species of bacterial cells in biofilm, while the lingonberry extract showed some antibiofilm effect on S. enterica serovar Senftenberg. In conclusion, finding natural plant products that are effective against biofilms formed by Gram-negative bacteria is still challenging.

Multidrug-resistant and extended-spectrum beta-lactamase-producing Enterobacteriaceae isolated from chicken droppings in poultry farms at Gondar City, Northwest Ethiopia

BACKGROUND

The poultry sector is one of the largest and fastest-growing agricultural sub-sector, especially in developing countries like Ethiopia. In poultry production, poultry farmers use sub-optimum doses of antibiotics for growth promotion and disease prevention purpose. This indiscriminate use of antibiotics in poultry farms contributes to the emergence of antibiotic-resistant bacteria, which has adverse implications for public health. Therefore, this study is aimed to assess multidrug resistance and extended-spectrum beta-lactamase-producing Enterobacteriaceae from chicken droppings in poultry farms.

METHODS

A total of 87 pooled chicken-dropping samples were collected from poultry farms from March to June 2022. Samples were transported with buffered peptone water. Selenite F broth was used for the enrichment and isolation of Salmonella spp. Isolates were cultured and identified by using MacConkey agar, Xylose lysine deoxycholate agar, and routine biochemical tests. Kirby-Bauer disk diffusion technique and combination disk test were used for antibiotic susceptibility testing and confirmation of extended-spectrum beta-lactamase production, respectively. Data were entered using Epi-data version 4.6 and then exported to SPSS version 26 for analysis.

RESULT

Out of 87 pooled chicken droppings, 143 Enterobacteriaceae isolates were identified. Of these, E. coli accounts for 87 (60.8%), followed by Salmonella spp. 23 (16.1%), P. mirabilis 18 (12.6%) and K. pneumoniae 11 (7.7%). A high resistance rate was observed for ampicillin 131 (91.6%), followed by tetracycline 130 (90.9), and trimethoprim-sulfamethoxazole 94 (65.7%). The overall multidrug resistance rate was 116/143 (81.1%; 95% CI: 74.7-87.5). A total of 12/143 (8.4%; CI: 3.9-12.9) isolates were extended-spectrum beta-lactamase producers, with 11/87 (12.6%) E. coli and 1/11 (9.1%) K. pneumoniae.

CONCLUSION AND RECOMMENDATIONS

High prevalence of multi-drug resistant isolates was observed. This study alarms poultry as a potential reservoir of extended-spectrum beta-lactamase-producing Enterobacteriaceae, which might shed and contaminate the environment through faecal matter. Prudent use of antibiotics should be implemented to manage antibiotic resistance in poultry production.

Comparative molecular profiling of antimicrobial resistance and phylogenetic characterization of multidrug-resistant Escherichia coli isolated from meat sources in 2009 and 2021 in Japan

The global spread of antimicrobial resistance (AMR) is alarming. Escherichia coli is a Gram-negative bacterium that causes healthcare-associated infections and is a major threat to public health. Currently, no comprehensive antimicrobial surveillance of multidrug-resistant E. coli of diverse phylogroups along the meat value chain has been implemented in Higashihiroshima, Japan. Therefore, by employing the One Health approach, 1183 bacterial isolates, including 303 recovered from meat samples in 2009, were screened for the presence of antimicrobial resistance determinants using multiplex PCR and DNA sequencing techniques. Seventy-seven non-duplicate E. coli isolates that harbored AMR genes were subjected to antimicrobial susceptibility testing and the detection of integrons. Phylogenetic characterization, which has not been previously investigated, was used to assign E. coli to one of the eight phylogroups. Twenty-six out of 33 (78.8%) and 34 out of 44 (77.3%) E. coli isolates from 2009 and 2021 exhibited multidrug resistance (MDR) phenotypes, respectively. The most common clinical resistance was observed against ampicillin, tetracycline, kanamycin, sulfamethoxazole/trimethoprim, cefotaxime, and chloramphenicol. Overall, 22.1% (17/77) of the E. coli isolates carried extended-spectrum β-lactamase (ESBL)-encoding genes and showed the ESBL-resistant phenotypes. For the two isolation years, AmpC/ESBL prevalence decreased from 42.4% in 2009 to 20.5% in 2021. The identified AMR genes included bla_CTX-M-1, bla_CTX-M-2, bla_CTX-M-14, bla_CTX-M-15, and bla_SHV-12 (ESBL-types); bla_SHV-1, bla_TEM-1, bla_TEM-135, and bla_TEM-176 (narrow-spectrum types); bla_CMY-4, bla_ADC-32, bla_ADC-216, bla_ACT-48, and bla_ACT-51 (AmpC types); and integrons. All E. coli isolates were negative for carbapenemase-encoding genes, whereas one isolate from 2009 carried mcr-5.1 allele. Approximately 52% of E. coli isolates identified in 2009 were assigned to phylogroup A compared to the 20.5% in 2021. Notably, the highest proportions of E. coli phylogroups exhibiting MDR were groups A, B1, and F, suggesting that members of these groups are mostly associated with drug resistance. This study highlights the role of meat as a significant reservoir of MDR E. coli and potential source for transmission of AMR genes. Our findings emphasize the importance of continuous monitoring to track the changes in the spread of antimicrobial resistance in the food chain.