Prevalence of specific serogroups, antibiotic resistance and virulence factors of avian pathogenic Escherichia coli (APEC) isolated from clinical cases: A systematic review and meta-analysis

Safety and efficacy of an inactivated tetravalent water-in-oil emulsion Escherichia coli vaccine against the E. coli peritonitis syndrome

RESEARCH HIGHLIGHTS

Protection against E. coli (EPS) challenge seems to be genotype-serotype-specific.Genotype B (O78:H4) gave (almost) full protection against genotypes B, F and H (all O78:H4).Genotype D (O11:H12) incited partial protection.Genotypes A (O1:H7) and C (O2:H1) were not protective.

Investigation of the anti-inflammatory mechanisms of fermented Chinese herbal residue solution in an APEC-Infected HD11 cell model through the PI3K/AKT and NF-κB pathways

Avian pathogenic Escherichia coli (APEC) infection poses a significant challenge to the poultry industry, severely threatening poultry health and industrial development. The emergence of antibiotic resistance in conventional treatments underscores the urgent need for novel alternative therapies. Fermented Chinese herbal residue solution, as a potential substitute, is rich in bioactive components and exhibits multifaceted effects, including anti-inflammatory, antioxidant, and immunomodulatory properties. This study investigates the anti-inflammatory mechanisms and key active compounds of the fermented herbal residue solution (BY3) in an APEC infection model. An in vitro APEC-infected HD11 cell model was established, with optimal infection conditions determined as a multiplicity of infection (MOI) of 0.1 and an infection duration of 6 hours, based on cytotoxicity assays and qPCR analysis. Results demonstrated that BY3 intervention significantly downregulated the expression of inflammatory cytokines. APEC infection markedly upregulated the expression of key target genes in the PI3K/AKT and NF-κB pathways, whereas BY3 treatment significantly reduced their expression. Western blot analysis further confirmed that BY3 significantly decreased the phosphorylation levels of AKT, P65, and IκB proteins, as well as the total PI3K protein content. These findings suggest that BY3 mitigates APEC-induced inflammation by modulating the PI3K/AKT and NF-κB pathways. To elucidate the active components of BY3, non-targeted metabolomics sequencing, database comparison, and molecular docking were employed, identifying four key bioactive compounds: Tangeretin, Arctigenin, Rhein, and Phloretin. All tested compounds significantly reduced APEC-induced inflammatory cytokine expression. qPCR and Western blot analyses revealed differential regulatory effects on the PI3K/AKT and NF-κB pathways. In the PI3K/AKT pathway, Tangeretin exhibited the most comprehensive inhibitory effect, significantly reducing both AKT phosphorylation and total PI3K levels. In the NF-κB pathway, all compounds except Rhein markedly decreased the phosphorylation of P65 and IκB. Collectively, BY3 and its identified compounds exert protective effects against APEC-induced HD11 cell damage by regulating the PI3K/AKT and NF-κB pathways, suggesting that the fermented Chinese herbal residue solution may represent a promising therapeutic approach for APEC-related diseases in poultry.

Identification of Virulence Genes and Antibiotic Resistance in Extraintestinal Pathogenic Escherichia coli Isolated from Broiler Carcasses Using MALDI-TOF MS

Escherichia coli contamination in poultry is a significant concern due to its potential to cause foodborne illness. The presence of extraintestinal pathogenic E. coli (ExPEC) strains in chicken carcasses can lead to severe human infections. This study investigates the prevalence, virulence, and antibiotic resistance of E. coli isolates from chicken carcasses processed in both wet market and industrial environments, with a focus on the detection capabilities of MALDI-TOF MS. A total of 119 E. coli isolates were obtained. Only a small proportion (5/119) carried enteropathogenic virulence genes. In contrast, 71.42% (85/119) of the isolates harbored multiple extraintestinal virulence genes. Among these, iucC and sitA, which are associated with systemic infections, were present in 68.24% (58/85) and 43.53% (37/85) of the isolates, respectively. Furthermore, 47.06% (56/119) of the isolates carrying at least two extraintestinal virulence genes were classified as ExPEC. Additionally, 94.6% (54/56) of ExPEC isolates were multidrug resistant (MDR), showing resistance to over three antibiotic classes, raising concerns about the spread of antibiotic resistance. MALDI-TOF MS profiling revealed significant heterogeneity among the ExPEC isolates, with no distinct clustering patterns based on processing environment or sampling site. These findings underscore the public health risks posed by ExPEC in poultry and emphasize the need for improved surveillance, stringent hygiene practices, and responsible antibiotic use in poultry production.

Molecular Characterization, Antibiotic Resistance, and Biofilm Formation of Escherichia coli Isolated from Commercial Broilers from Four Chinese Provinces

Escherichia coli (E. coli) represents a significant etiological agent of colibacillosis in poultry, resulting in considerable economic losses for the global poultry sector. The present study aimed to determine molecular characterization, antibiotic resistance, and biofilm formation of E. coli strains isolated from diseased broilers from four provinces of China. A total of 200 tissue samples were collected from the intestine, liver, crop, heart, and spleen and processed for microbiological examination. Molecular detection of E. coli strains, virulence genes, and serotypes was performed using polymerase chain reaction (PCR). Antibiotic susceptibility testing and biofilm formation were assessed using disk diffusion and 96-well microtiter plate assays. The study retrieved 68% (136/200) of E. coli strains from collected samples. Most of the E. coli strains were resistant to enrofloxacin (56%), followed by cefepime (54%), amoxicillin/clavulanate (52%), streptomycin (50%), ampicillin (48%), clindamycin (47%), kanamycin (41%), polymyxin B (37%), tetracycline (35%), sulfamethoxazole/trimethoprim (33%), ceftazidime (31%), meropenem (4.7%), and florfenicol (2.9%). Similarly, the E. coli strains tested positive for at least one virulence gene and specific serotypes. Among these, O145 was the most prevalent serotype, identified in 22 isolates (16.2%), followed by O8 (12.5%), O102 (11.8%), and O9 (11.0%). The tsh gene (10.2%) was the most prevalent virulence gene. This study found that 47.1% of E. coli strains were biofilm-producing, with 62.5% exhibiting weak biofilm production, 29.7% mild biofilm production, and 7.8% strong biofilm production. Similarly, 24.2% of the E. coli strains were avian pathogenic E. coli strains due to the presence of five or more virulence genes, specifically tsh, ompA, fimC, iss, fyuA, and astA, in a single strain by multiplex PCR. The present study recommends continuous surveillance and effective control measures to reduce the burden of avian pathogenic E. coli-related infections in poultry.

Drug resistance and pathogenicity characteristics of Escherichia coli causing pneumonia in farmed foxes

Bacterial pneumonia is a leading cause of mortality in fur-bearing animals, posing significant threat to fur production. To clarify the pathogenic agent of bacterial pneumonia in farmed foxes from eastern Hebei province, China, we performed bacterial isolation and identification from samples between 2020 and 2023. A total of 142 bacterial strains were isolated, of which 101 were identified as Escherichia coli (E. coli), indicating that E. coli is the major cause responsible for bacterial pneumonia in farmed foxes. Serotyping identification showed that a total of 8 serotypes were prevalent in the E. coli isolates, with O1, O8, O78 and O12 being the dominant ones. Five E. coli isolates were randomly picked for pathogenicity testing, and all of them were able to cause pneumonia symptoms in 6-week-old Kunming mice, accompanied by organ damage in lung. Eleven virulence genes were demonstrated present among the E. coli isolates. Antibiotic susceptibility tests showed that 78 of 101 E. coli strains exhibited multi-drug resistance (MDR), with the highest resistance rates against tetracyclines, and some strains showed resistance to carbapenems. Notably, no single antibiotic was effective against all strains. Twenty antibiotic resistance genes (ARGs) were detected among the isolates. Multilocus sequence typing (MLST) revealed 11 sequence types (STs) among 19 E. coli isolates, with ST-101 predominating (4/19). These findings enhance our understanding of the epidemiology, resistance traits, and pathogenicity of fox-derived pathogenic E. coli in Hebei.

Deep culturing the fecal microbiota of healthy laying hens

BACKGROUND

The microbiota is implicated in several aspects of livestock health and disease. Understanding the structure and function of the poultry microbiota would be a valuable tool for improving their health and productivity since the microbiota can likely be optimized for metrics that are important to the industry such as improved feed conversion ratio, lower greenhouse gas emissions, and higher levels of competitive exclusion against pathogens. Most research into understanding the poultry microbiota has relied on culture-independent methods; however, the pure culture of bacteria is essential to elucidating the roles of individual bacteria in the microbiota and developing novel probiotic products for poultry production.

RESULTS

In this study, we have used a deep culturing approach consisting of 76 culture conditions to generate a culture collection of 1,240 bacterial isolates from healthy chickens. We then compared the taxonomy of cultured isolates to the taxonomic results of metagenomic sequencing to estimate what proportion of the microbiota was cultured. Metagenomic sequencing detected DNA from 545 bacterial species while deep culturing was able to produce isolates for 128 bacterial species. Some bacterial families, such as Comamonadaceae and Neisseriaceae were only detected via culturing - indicating that metagenomic analysis may not provide a complete taxonomic census of the microbiota. To further examine sub-species diversity in the poultry bacteriome, we whole genome sequenced 114 Escherichia coli isolates from 6 fecal samples and observed a great deal of diversity.

CONCLUSIONS

Deep culturing and metagenomic sequencing approaches to examine the diversity of the microbiota within an individual will yield different results. In this project we generated a culture collection of enteric bacteria from healthy laying hens that can be used to further understand the role of specific commensals within the broader microbiota context and have made this collection available to the community. Isolates from this collection can be requested by contacting the corresponding author and will be provided at cost.

An insight into newly emerging avian pathogenic E. coli serogroups, biofilm formation, ESBLs and integron detection and in vivo pathogenicity in chicken

Bacterial diseases alone or in combination with other pathogens lead to significant economic losses in poultry globally including India. One of these diseases is avian colibacillosis which is caused by avian pathogenic Escherichia coli (APEC). The present study sought to isolate and characterize using in vivo and in vitro assays E. coli recovered from poultry diagnosed with colibacillosis. A total of 55 E. coli isolates were recovered from tissues of 55 broiler flocks affected with colibacillosis by using standard microbiological techniques, Vitek 2 Compact system and polymerase chain reaction. Out of 55 E. coli isolates, 50 (90.9 %) were characterized as APEC by multiplex PCR using a set of five virulence genes. On serotyping, 16 (32 %) APEC isolates were serogrouped as O26 followed by O98 (28 %), O120 (14 %), O11 (12 %), O135 (8 %) and O17 (4 %). The antimicrobial susceptibility testing of E. coli isolates revealed high antibiotic resistance against imipenem, tetracycline, ciprofloxacin and levofloxacin (96 % each). Interestingly all the 50 suspect APEC isolates were found to be multiple drug resistant (MDR) and the antimicrobial profiling indicated that these isolates could be classified into 38 resistotypes. Moreover, 10 (20 %) isolates were ESBL producers as per phenotypic characterization using combined disk diffusion test. On genotypic characterization of ESBLs, 31 (62 %) isolates were found positive for the blaTEM gene, whereas, 34 (68 %) isolates carried intI1 gene. On assessment for biofilm formation at 72 h incubation, thirteen (26 %) isolates were found to be strong biofilm producers, whereas nine (18 %) and twenty-eight (56 %) isolates were moderate and weak biofilm producers, respectively. Later, the LD50 of one MDR and strong biofilm producing isolate (APEC-P02) was calculated by in vivo oral challenge study in day old broiler chicks. The findings of this study demonstrated that LD50 of APEC-P02 isolate was 1.12 × 108 CFU/ml. The unexpectedly high prevalence of O11, O126, O98, O120 and O135 isolates suggest that there may be emergent serogroups causing colibacillosis in India. The current oral challenge study seems to be the first of its kind in India to estimate the LD50 of a multidrug resistant biofilm producer APEC isolate in day-old chicks.

Molecular Epidemiology and Antibiotic Resistance Associated with Avian Pathogenic Escherichia coli in Shanxi Province, China, from 2021 to 2023

Avian Pathogenic Escherichia coli (APEC) constitutes a major etiological agent of avian colibacillosis, which significantly hinders the development of the poultry industry. Conducting molecular epidemiological studies of APEC plays a crucial role in its prevention and control. This study aims to elucidate the molecular epidemiological characteristics of Avian Pathogenic Escherichia coli in Shanxi Province. In this study, 135 APEC strains were isolated and identified from 150 liver samples of diseased and deceased chickens exhibiting clinical symptoms, which were collected from farms in Shanxi Province between 2021 and 2023. The isolates were then analyzed for phylogenetic clustering, drug resistance, resistance genes, virulence genes, and biofilm formation capabilities. The results revealed that the proportions of the A, B1, B2, and D evolutionary subgroups were 26.67%, 32.59%, 17.78%, and 15.56%, respectively. The drug resistance testing results indicated that 92% of the isolates exhibited resistance to cotrimoxazole, kanamycin, chloramphenicol, amoxicillin, tetracycline, and other antibiotics. In contrast, 95% of the strains were sensitive to ofloxacin, amikacin, and ceftazidime. The most prevalent resistance genes included tetracycline-related (tetA) at 88.15%, followed by beta-lactam-related (bla-TEM) at 85.19%, and peptide-related (mcr1) at 12.59%. The virulence gene analysis revealed that ibeB, ompA, iucD, and mat were present in more than 90% of the isolates. The results revealed that 110 strains were biofilm-positive, corresponding to a detection rate of 81.48%. No significant correlation was found between the drug resistance genes, virulence genes, and the drug resistance phenotype. A moderate negative correlation was observed between the adhesion-related gene tsh and biofilm formation ability (r = -0.38). This study provides valuable insights into the prevention and control of avian colibacillosis in Shanxi Province.

Longitudinal analysis of avian pathogenic Escherichia coli (APEC) serogroups and pathotypes from avian colibacillosis in Georgia: A continued investigation - year 2 analysis

Avian pathogenic Escherichia coli (APEC) is a significant cause of worldwide morbidity, mortality, and production loss in the poultry industry. Here, we characterized 115 E. coli isolates from avian-diagnosed colibacillosis cases from Georgia, USA in 2022 as part of a year two follow on surveillance using both current and a newly developed serogrouping tool (Klao9-SeroPCR). The isolates examined were classified into 18 serogroups with the majority classifying as O78, O25, O86, O2, O8, and O1 with 32 isolates classified as untypable serogroups. In this study, the Klao9-seroPCR was able to identify serogroups of 72/115 isolates (62.6 %) using the multiplex PCR assay. This diagnostic PCR assay proved to be a potential technique for the rapid identification of the most common APEC serogroups dominating in Georgia poultry. Genotyping based on detection of selected virulence genes (VAGs) found that 22.6 % of isolates did not harbor any of the targeted genes. This analysis also confirmed that the CoIV plasmid-associated genes (iroN, ompT, hlyF, iss, and aerJ,) are still frequently found among APEC isolates (54-65 %) with a slightly lower prevalence compared to the previous year's study. Phylogenetic analysis showed that the isolates belong to phylogenetic groups G (43 %), group B2 (13 %), group F (6 %), and group A (5 %). Of interest, 30 % were identified as an unknown or cryptic phylogenetic group. This study highlights that there is a shift in the APEC causing disease in birds in the state of Georgia with virulence commonly associated with the presence of the CoIV plasmid in disease strains. Of interest, the new serogrouping panel that is designed to target more common serogroups seen in Georgia has proven to be a rapid screening/ diagnostic tool for implementation in our workflow. This study highlights a need to continue to monitor the APEC serogroups in the field to apply appropriate preventive plans against colibacillosis.

The transcription factor YbdO attenuates the pathogenicity of avian pathogenic Escherichia coli by regulating oxidative stress response

Avian pathogenic Escherichia coli (APEC) is a significant pathogen infecting poultry that is responsible for high mortality, morbidity and severe economic losses to the poultry industry globally, posing a substantial risk to the health of poultry. APEC encounters reactive oxygen species (ROS) during the infection process and thus has evolved antioxidant defense mechanisms to protect against oxidative damage. The imbalance of ROS production and antioxidant defenses is known as oxidative stress, which results in oxidative damage to proteins, lipids and DNA, and even bacterial cell death. APEC uses transcription factors (TFs) to handle oxidative stress. While many TFs in E. coli have been well characterized, the mechanism of the YbdO TF on protecting against oxidative damage and regulating the virulence and pathogenicity of APEC has not been clarified. Here we focus on the regulatory mechanism of YbdO on the pathogenicity of APEC. The results from this study showed that YbdO attenuated the pathogenicity of APEC in chicks infection models by inhibiting the expression of virulence genes fepG and ycgV using quantitative real-time reverse transcription PCR (RT-qPCR) experiments. The electrophoretic mobility shift assays (EMSA) confirmed that YbdO specifically bound to the promoters of fepG and ycgV. Additionally, YbdO increases H2O2-induced oxidative damage to APEC via repressing the expression of oxidative stress response genes sodA, soxR, ahpC, ahpF, katG, and oxyR by binding to their promoter regions. The repression effect facilitates host immune response to eliminate APEC and to generate beneficial immune protection to the body, thereby indirectly attenuating the pathogenicity of APEC. These findings might provide further insights into the mechanism of oxidative damage to APEC and offer new perspectives for further studies on the prevention and control of APEC infections.