Refining the definition of the avian pathogenic Escherichia coli (APEC) pathotype through inclusion of high-risk clonal groups

Avian pathogenic Escherichia coli (APEC) isolated from chicks and embryos in the hatchery

Avian pathogenic Escherichia coli (APEC) is the most common cause of omphalitis. This disease affects newborn chicks up to the 7th day of life, causing high mortality and reduced performance of broilers. The study aimed to determine the frequency of APEC occurrence in embryos and newly hatched chicks. E. coli isolates were subjected to PCR to identify the minimal predictive virulence factors, phylogenetic groups, and predictive identification of the clonal complex (CC) ST131, ST117, and ST95. The phenotypic analysis assessed the antimicrobial resistance profile. A total of 254 samples were analyzed and 60.63% (n = 154/254) were positive for E. coli, of which 35.71% (n = 55/154) were classified as APEC (60% (n = 33/55) isolated in the yolk sac of day-old chicks, 29.09% (n = 16/55) in pipped eggs and 10.91% (n = 6/55) in embryonated eggs). The B2 phylogenetic group accounted for 21.81% (n = 12/55), with an increase in the contamination by B2 strains during the incubation process, from 6.25% (n = 1) to 30.30% (n = 10). We also identified 14.54% (n = 8/55) strains for the G group. The sequence types ST131 and ST117 were observed at the same frequency (10.90%, n = 6), followed by ST95 (3.6%, n = 2). A total of 27.27% were considered multidrug-resistant strains (MDR). The highest resistance rate was amoxicillin (43.64%, n = 24) and tetracycline (25.45%, n = 14). To a lesser extent, levels of resistance to critical drugs commonly used in hatcheries were identified, such as ceftiofur (20%, n = 11) and gentamicin (7%, n = 4).

Longitudinal study of avian pathogenic Escherichia coli (APEC) serogroups associated with disease in Georgia poultry using molecular serology and virulence gene analysis

Avian pathogenic Escherichia coli (APEC) is a significant cause of morbidity, mortality, and production loss to the poultry industry worldwide. Here, we characterized 569 E. coli isolates from avian-diagnosed colibacillosis cases from the state of Georgia, USA. In total, 339 isolates were assigned into 32 serogroups with the majority classifying as O78, O2, O25, O8, O1, O86, O18, and O15. Serogroup O25 was found to link with broilers, while broiler breeders were more often associated with serogroup O1 and pet/ hobby birds with serogroup O8. In addition, some serogroups (O1) were more prevalent in the summer and fall. Analysis for virulence-associated genes (VAGs) found 23.20% of isolates did not harbour any genes linked with the APEC pathotype, while ColV plasmid-associated genes (iroN, ompT, hlyF, iss, and aerJ) were frequently detected among most isolates (with 80-96% prevalence) and some of these genes were linked with serogroup. Phylogenetic analysis, classified isolates into phylogenetic groups B2 (34%), F (19%), A (15%), and G (9%). The phylogenetic group B2 isolates also harboured the highest number of VAGs. This study highlights that the current APEC-causing disease in birds in the State of Georgia has identified several emerging serogroups possessing several VAGs that could potentially lead to challenges in colibacillosis control.RESEARCH HIGHLIGHTSSeveral emerging APEC serogroups were observed in Georgia poultry populations.An association between APEC serogroups and bird type was observed.The prevalence of different APEC serogroups was influenced by season.A multiplex PCR assay targeting common serogroups of APEC in Georgia poultry was developed.

Development of a bacteriophage cocktail with high specificity against high-risk avian pathogenic Escherichia coli

Avian pathogenic Escherichia coli (APEC) is a widespread pathogen that poses a significant threat to the poultry industry globally. A recent typing scheme has proposed several APEC pathotypes, including non-APEC, High Risk non-APEC (HR non-APEC), APEC, and High Risk APEC (HR APEC), based on the presence of the ompT and hlyF genes, sequence types (ST) ST131, ST23, ST428, ST355, and the O78 antigen. In Brazilian broiler farms, a higher prevalence of lesions in carcasses has been linked to the presence of HR APEC pathotypes. Due to the growing concern over antimicrobial resistance, bacteriophage-based formulations are emerging as a promising alternative for controlling APEC outbreaks. In this study, we isolated and sequenced 142 strains from Brazilian commercial broiler farms, classifying them as APEC (70), HR APEC (12), HR non-APEC (3) and non-APEC (57). Notably, 38 % of the isolates were classified as multi-drug resistant (MDR), with serotypes H10 and ST155 being the most frequently identified. Additionally, we isolated, sequenced, and classified 66 bacteriophages that exhibited lytic activity against these bacterial strains in both qualitative and quantitative assays. Eight of the bacteriophages demonstrated complementary host ranges against the bacterial collection. Bacteriophage cocktails were assembled, tested in quantitative assays, and shown to be effective against APEC. A cocktail consisting of four bacteriophages (AC-01) displayed a broad lytic spectrum in vitro, inhibiting the growth of 56.3 % (n = 80/142) of the isolates with a mean inhibition of 32.9 %. Remarkably, the in vitro lytic activity of the cocktail was significantly more effective against HR APEC isolates (12/12, 65.9 % mean inhibition) and HR non-APEC isolates (3/3, 58.0 % mean inhibition). Our results emphasize the importance of genetically characterizing target bacteria when developing an effective and specific bacteriophage cocktail against APEC.

Integrated Transcriptome Analysis Reveals the Lung miRNA-mRNA Regulatory Network Associated with Avian Pathogenic E. coli Infection

Avian pathogenic E. coli (APEC), one of the most common pathogens, can cause localized or systemic infections and lead to significant economic losses in the poultry industry annually. Recently, evidence suggests that microRNAs (miRNAs) play important roles in the host immune response to bacterial infection by targeting mRNAs. However, few studies have examined the immune mechanisms of miRNAs and mRNAs in chicken lungs following APEC infection. Herein, hematoxylin-eosin staining and qRT-PCR were employed to investigate APEC-induced lung inflammation in chickens. RNAseq was used to identify the miRNAs and mRNAs expression profile between the APEC infection group (APEC) vs. the Control group (Control). The results show that APEC can induce lung lesions in chickens and increase the expression levels of inflammatory cytokines (IL1β, IL8, IL6, and TNFα). High-quality sequencing data were obtained, of which more than 93% of the reads can be mapped to the chicken genome. A total of 22 differentially expressed (DE) miRNAs and 608 DE mRNAs were detected in the APEC vs. the Control. Remarkably, 23 regulatory pairs of miRNA-mRNA interactions were identified in chicken lungs upon APEC infection. Further validation revealed that gga-miR-214 could directly target the RAB37 gene upon APEC infection to modulate the expression of inflammatory cytokine response. This study provides new insights into the host immune response to APEC infection.

The pathogenicity traits of avian pathogenic Escherichia coli O25-ST131 associated with avian colibacillosis in Georgia poultry and their genotypic and phenotypic overlap with other extraintestinal pathogenic E. coli

AIMS

To characterize Escherichia coli O25 ST131 (O25-ST131) isolated from Georgia poultry-a "global high-risk" clonal strain.

METHODS AND RESULTS

Using multiplex PCR to detect target genes in 98 isolates of avian pathogenic E. coli (APEC) O25 recovered from avians diagnosed with colibacillosis (n = 87) and healthy chicks (n = 11) in Georgia, USA. Eighty-eight isolates were classified as sequence type ST131 clade b and 56% (n = 49) belong to the phylogenetic group B2. Overall, 17% were identified as uropathogenic E. coli (UPEC)-like and 94% of the isolates formed strong to moderate biofilms. The extended-spectrum β-lactamases encoding genes, blaCTX M-15 (24%), carbapenemases encoding genes, and blaOXA48 (16%) were also detected. The isolates harbored FIB (88%), FIC (28%), A/C (14%), and FIIA (6%) plasmid replicons. Interestingly, 78% of the isolates were found to be resistant to chicken serum and 92% showed capabilities for growth in human urine. The isolates showed phenotypic resistance to several antibiotics including chloramphenicol (63%), ciprofloxacin (57%), trimethoprim-sulfamethoxazole (28%), streptomycin (17%), and cefoxitin and meropenem (14%) using the national antimicrobial resistance monitoring system panel.

CONCLUSIONS

Overall, our study provides evidence of the virulence of these global "high-risk" clones in Georgia poultry with some isolates showing genotypic overlap between APEC and UPEC. Also, this clone harbored several virulence genes, antimicrobial-resistant genes, and plasmids. Interestingly, the majority of APEC O25-ST131 isolates can survive and grow in both chicken serum and human urine and warrant further investigation of their potential pathogenicity for both chickens and humans.

Coupling antitoxins and blue/white screening with parAB/resolvase mutation as a strategy for Salmonella spp. plasmid curing

Despite the dissemination of multidrug resistance plasmids, including those carrying virulence genes in Salmonella spp., efficient plasmid curing tools are lacking. Plasmid partitioning and multimer resolution systems are attractive targets for plasmid cure. However, plasmid curing strategies targeting these systems are often hindered by the host addiction system through a process known as post-segregation killing. Here, we developed vector tools that can mutate the above systems while replenishing short-lived antitoxins. Cloning was performed using Gibson assembly. parAB or resolvase (res) genes on Incompatibility Group (Inc)FIB, IncA/C, IncX4, and plasmids carried by Salmonella species were deleted by first knocking in the N-terminal ß-galactosidase encoding gene (bgaB), followed by in-frame insertion of its C-terminal region using pDG1 and pDG2 vectors, respectively. pDG1 was used as a backbone to develop a vector, designated as pDG-At, expressing 13 antitoxins driven by strong promoters. Plasmid curing was achieved by transforming pDG-At to parAB or res mutants followed by blue-white screening and PCR; however, parAB mutant isolation with this method was low and often non-reproducible. To elucidate whether the prior presence of pDG-At in cells improves viable mutant isolation, we re-constructed pDG-At, designated as pDG-Atπ, using a vector with the R6Kϒ origin of replication with its π-factor required for replication under araBAD promoter. Results showed that pDG-Atπ can replicate in the absence of arabinose but can be cured by growing cells in glucose-rich media. Next, we repeated IncFIB's parAB deletion using pDG1 but in cells carrying pDG-Atπ. Many white colonies were detected on X-Gal-supplemented media but none of them carried the target parA mutation; however, ~80% of the white colonies lost IncFIB plasmid, while the others retained the wild-type plasmid. Similar results were obtained for IncX4 plasmid curing but also found that this method was not reproducible as the white colonies obtained after allelic replacement did not always result in plasmid curing or mutant isolation. This is the first report describing a simple blue/white screening method for plasmid curing that can avoid laborious screening procedures.

IMPORTANCE

Plasmids play an important role in bacterial physiology, adaptation, evolution, virulence, and antibiotic resistance. An in-depth study of these roles partly depends on the generation of plasmid-free cells. This study shows that vector tools that target genes required for plasmid stability in the presence of an antitoxin-expressing helper plasmid are a viable approach to cure specific plasmids. Expression of bgaB from target plasmids can greatly facilitate visual detection of plasmid cured colonies avoiding time-consuming screening procedures. This approach can be refined for the development of a universal plasmid curing system that can be used to generate plasmid-free cells in other human bacterial pathogens including Gram positives and Gram negatives.

The multifaceted role of TolA protein in promoting survival, biofilm formation and virulence of avian pathogenic Escherichia coli

Avian pathogenic Escherichia coli (APEC) can spread beyond the intestines and cause systemic infections, leading to various clinical manifestations, including airsacculitis, pericarditis, perihepatitis and colisepticemia. The mechanisms facilitating this extraintestinal infections are not fully understood. In this study, we investigate how the tolA gene affects APEC virulence by encoding a protein involved in maintaining outer membrane integrity. We constructed a tolA deletion mutant of APEC strain E058 and evaluated its growth and survival in various environments, including in vitro cultures and in vivo infection models in chickens. We found that the motility-defective ΔtolA mutant exhibits reduced biofilm formation ability and weakened resistance to the environmental stresses, suggesting an important role for TolA in APEC's survival. The lack of tolA gene affects the bacterial ability to resist the host's immune system, such as complement-mediated serum killing or phagocytosis, as shown by the serum killing and macrophage phagocytosis assays. Additionally, in vivo infection studies using chickens demonstrated that the ΔtolA mutant displayed attenuated virulence, evidenced by reduced mortality and lower tissue bacterial burden. Reverse transcription quantitative real-time PCR (RT-qPCR) analysis revealed that inactivation of tolA led to downregulation of virulence genes associated with serum resistance (traT) and flagellar biosynthesis (fliR). Taken together, our findings demonstrate the multifaceted role of TolA protein in promoting the survival, immune evasion, biofilm formation, and virulence of APEC E058. This suggests that targeting TolA could potentially offer new strategies for combating APEC infections.

Isolation and Characterization of Escherichia coli from Brazilian Broilers

Avian pathogenic Escherichia coli (APEC) causes colibacillosis, one of the main diseases leading to economic losses in industrial poultry farming due to high morbidity and mortality and its role in the condemnation of chicken carcasses. This study aimed to isolate and characterize APEC obtained from necropsied chickens on Brazilian poultry farms. Samples from birds already necropsied by routine inspection were collected from 100 batches of broiler chickens from six Brazilian states between August and November 2021. Three femurs were collected per batch, and characteristic E. coli colonies were isolated on MacConkey agar and characterized by qualitative PCR for minimal predictive APEC genes, antimicrobial susceptibility testing, and whole genome sequencing to identify species, serogroups, virulence genes, and resistance genes. Phenotypic resistance indices revealed significant resistance to several antibiotics from different antimicrobial classes. The isolates harbored virulence genes linked to APEC pathogenicity, including adhesion, iron acquisition, serum resistance, and toxins. Aminoglycoside resistance genes were detected in 79.36% of isolates, 74.6% had sulfonamide resistance genes, 63.49% showed β-lactam resistance genes, and 49.2% possessed at least one tetracycline resistance gene. This study found a 58% prevalence of avian pathogenic E. coli in Brazilian poultry, with strains showing notable antimicrobial resistance to commonly used antibiotics.

Horizontal transfer characterization of ColV plasmids in blaCTX-M-bearing avian Escherichia coli

Extended-spectrum-β-lactamases (ESBLs)-producing Escherichia coli conferred resistance to most β-lactams, except for carbapenems. To date, the transmission mechanism of blaCTX-M, as the most common ESBLs subtype, in E. coli has received sustained attention around the worldwide, but the research on the pathogenicity of blaCTX-M-bearing E. coli is still scarce. The aims of this study were to discern the spread characteristics of ColV (encoding colicin V) plasmids in blaCTX-M-positive E. coli. The multi-drug resistance traits, phylogroups, and ColV plasmid profilings were screened in 76 blaCTX-M-positive E. coli. Thereafter, the genetic profiles of E. coli G12 and GZM7 were determined by whole genome sequencing, conjugation and S1-pulsed-field gel electrophoresis. The median lethal dose was analyzed in E. coli G12 and TG12A, the ColV-plasmid transconjugant of G12. Of all 76 blaCTX-M-bearing E. coli, 67.11% exhibited resistance to at least 2 drugs in addition to ceftiofur, 14.47% carried ColV-positive plasmids, and 53.95% were phylogroup C. Further studies demonstrated that the blaCTX-M-bearing E. coli G12 was assigned to the predominant lineage O78:H4-ST117 of phylogroup G. In addition, its ColV-positive plasmid simultaneously carried multiple resistance genes, and could be independently transferred to confer partial pathogenicity on its host by plasmid mating. E. coli GZM7 was O53:H9-ST23 of phylogroup C, which belonged to another representative lineage of APEC (avian pathogenic E. coli). Its ColV-positive plasmid could complete conjugation with the help of the other coexisting-resistance conjugative plasmid, although it failed to transfer alone. Our findings highlight the flexibly horizontal transfer of ColV plasmids along with multidrug-resistant genes among blaCTX-M-bearing E. coli poses a threat to poultry health and food safety, which contributes to elucidate the concept of "One Health" and deserves particular concern.

A comprehensive study of colisepticaemia progression in layer chickens applying novel tools elucidates pathogenesis and transmission of Escherichia coli into eggs

Colisepticaemia caused by avian pathogenic Escherichia coli (APEC) is a challenging disease due to its high economic importance in poultry, dubious pathogenesis and potential link with zoonosis and food safety. The existing in vitro studies can't define hallmark traits of APEC isolates, suggesting a paradigm shift towards host response to understand pathogenesis. This study investigated the comprehensive pathological and microbial progression of colisepticaemia, and transmission of E. coli into eggs using novel tools. In total 48 hens were allocated into three groups and were inoculated intratracheally with ilux2-E. coli PA14/17480/5-/ovary (bioluminescent strain), E. coli PA14/17480/5-/ovary or phosphate buffered saline. Infection with both strains led to typical clinical signs and lesions of colibacillosis as in field outbreaks. Based on lung histopathology, colisepticaemia progression was divided into four disease stages as: stage I (1-3 days post infection (dpi)), stage II (6 dpi), stage III (9 dpi) and stage IV (16 dpi) that were histologically characterized by predominance of heterophils, mixed cells, pyogranuloma, and convalescence, respectively. As disease progressed, bacterial colonization in host organs also decreased, revealed by the quantification of bacterial bioluminescence, bacteriology, and quantitative immunohistochemistry. Furthermore, immunofluorescence, immunohistochemistry, and bacteria re-isolation showed that E. coli colonized the reproductive tract of infected hens and reached to egg yolk and albumen. In conclusion, the study provides novel insights into the pathogenesis of colisepticemia by characterizing microbial and pathological changes at different disease stages, and of the bacteria transmission to table eggs, which have serious consequences on poultry health and food safety.

Clonal and plasmidic dissemination of critical antimicrobial resistance genes through clinically relevant ExPEC and APEC-like lineages (ST) in the dairy cattle population of Québec, Canada

Antimicrobial resistance can be effectively limited by improving the judicious use of antimicrobials in food production. However, its effect on the spread of AMR genes in animal populations is not well described. In the province of Québec, Canada, a new legislation implemented in 2019 has led to an unprecedented reduction in the use of critical antimicrobials in dairy production. We aimed to investigate the potential link between ESBL/AmpC E. coli isolated before and after legislation and to determine the presence of plasmids carrying genes responsible for critical AMR. We collected fecal samples from calves, cows, and manure pit from 87 Québec dairy farms approximately 2 years before and 2 years after the legislation came into effect. The whole genomes of 183 presumptive ESBL/AmpC E. coli isolated after cefotaxime enrichment were sequenced. Their phylogenetic characteristics (MLST, serogroup, cgMLST) and the presence of virulence and resistance genes and replicons were examined. A maximum likelihood phylogenetic tree was constructed based on single nucleotide polymorphism (SNPs). We identified 10 clonal lineages (same cgMLST) and 7 clones (SNPs ≤ 52). Isolates belonging to these clones could be found on different farms before and after the legislation, strongly suggesting a clonal spread of AMR genes in the population during this 4-year period. All isolates were multidrug resistant (MDR), with clone 2 being notable for the presence of macrolide, fluoroquinolone, and third-generation cephalosporin resistance genes. We also identified clinically relevant ExPEC (ST10) and APEC-like lineages (ST117, ST58, ST88) associated with the presence of ExPEC and APEC virulence genes, respectively. Our data also suggests the presence of one epidemic plasmid belonging to the IncY incompatibility group and carrying qnrs1 and blaCTX-M-15. We demonstrated that AMR genes spread through farms and can persist over a 4-year period in the dairy cattle population through both plasmids and E. coli clones, despite the restriction of critical antimicrobial use. MDR ExPEC and APEC-like STs are present in the normal microbiota of cattle (more frequently in calves). These data increase our knowledge on gene dissemination dynamics and highlight the fact that biosecurity measures should be enhanced in this industry to limit such dissemination.

Versatile allelic replacement and self-excising integrative vectors for plasmid genome mutation and complementation

IMPORTANCE

In spite of the dissemination of multidrug-resistant plasmids among Gram-negative pathogens, including those carrying virulence genes, vector tools for studying plasmid-born genes are lacking. The allelic replacement vectors can be used to generate plasmid or chromosomal mutations including markless point mutations. This is the first report describing a self-excising integrative vector that can be used as a stable single-copy complementing tool to study medically important pathogens including in vivo studies without the need for antibiotic selection. Overall, our newly developed vectors can be applied for the assessment of the function of plasmid-encoded genes by specifically creating mutations, moving large operons between plasmids and to/from the chromosome, and complementing phenotypes associated with gene mutation. Furthermore, the vectors express chromophores for the detection of target gene modification or colony isolation, avoiding time-consuming screening procedures.

Characteristics of antimicrobial resistance in Escherichia coli isolated from retail meat products in North Carolina

BACKGROUND

Escherichia coli is commonly used as an indicator for antimicrobial resistance (AMR) in food, animal, environment, and human surveillance systems. Our study aimed to characterize AMR in E. coli isolated from retail meat purchased from grocery stores in North Carolina, USA as part of the National Antimicrobial Resistance Monitoring System (NARMS).

MATERIALS AND METHODS

Retail chicken (breast, n = 96; giblets, n = 24), turkey (n = 96), and pork (n = 96) products were purchased monthly from different counties in North Carolina during 2022. Label claims on packages regarding antibiotic use were recorded at collection. E. coli was isolated from meat samples using culture-based methods and isolates were characterized for antimicrobial resistance using whole genome sequencing. Multi-locus sequence typing, phylogroups, and a single nucleotide polymorphism (SNP)-based maximum-likelihood phylogenic tree was generated. Data were analyzed statistically to determine differences between antibiotic use claims and meat type.

RESULTS

Of 312 retail meat samples, 138 (44.2%) were positive for E. coli, with turkey (78/138; 56.5%) demonstrating the highest prevalence. Prevalence was lower in chicken (41/138; 29.7%) and pork (19/138;13.8%). Quality sequence data was available from 84.8% (117/138) of the E. coli isolates, which included 72 (61.5%) from turkey, 27 (23.1%) from chicken breast, and 18 (15.4%) from pork. Genes associated with AMR were detected in 77.8% (91/117) of the isolates and 35.9% (42/117) were defined as multidrug resistant (MDR: being resistant to ≥3 distinct classes of antimicrobials). Commonly observed AMR genes included tetB (35%), tetA (24.8%), aph(3'')-lb (24.8%), and blaTEM-1 (20.5%), the majority of which originated from turkey isolates. Antibiotics use claims had no statistical effect on MDR E. coli isolates from the different meat types (X2 = 2.21, p = 0.33). MDR was observed in isolates from meat products with labels indicating "no claims" (n = 29; 69%), "no antibiotics ever" (n = 9; 21.4%), and "organic" (n = 4; 9.5%). Thirty-four different replicon types were observed. AMR genes were carried on plasmids in 17 E. coli isolates, of which 15 (88.2%) were from turkey and two (11.8%) from chicken. Known sequence types (STs) were described for 81 E. coli isolates, with ST117 (8.5%), ST297 (5.1%), and ST58 (3.4%) being the most prevalent across retail meat types. The most prevalent phylogroups were B1 (29.1%) and A (28.2%). Five clonal patterns were detected among isolates.

CONCLUSIONS

E. coli prevalence and the presence of AMR and MDR were highest in turkey retail meat. The lack of an association between MDR E. coli in retail meat and antibiotic use claim, including those with no indication of antimicrobial use, suggests that additional research is required to understand the origin of resistance. The presence of ST117, an emerging human pathogen, warrants further surveillance. The isolates were distinctly diverse suggesting an instability in population dynamics.

Veterinary Autogenous Vaccines for Poultry in Europe-Many Ways to Crack an Egg

In the past decade, European animal farming has increasingly used autogenous vaccines for the prevention of nonnotifiable diseases. In Europe, these vaccines are exclusively inactivated bacterial and viral vaccines, with a set of specific regulations that differentiate them from conventional vaccines. The highest number of applications most likely occurs in poultry, as these animal species are farmed in the highest numbers compared with other types of food-producing animals. In 2019, autogenous vaccines came within the scope of harmonized European regulation for the first time, although many important aspects are still missing and need to be further developed. Consequently, several important legal provisions remain in national legislations and can vary tremendously between different member states of the European Union. The inclusion of autogenous vaccines in the management of certain diseases of poultry is justified by the nonavailability of licensed vaccines and the evolution and diversity of antigens in the field that are not covered by licensed vaccines. In addition, these vaccines aid in reducing the use of antibiotics. The methods for isolating and typing pathogenic isolates to obtain relevant antigens are pathogen specific and require a careful approach based on clinical evidence. Manufacturing processes are optimized according to regulatory standards, and they represent the most critical factor influencing the quality of autogenous vaccines and their placement on the market. This review presents the important requirements for manufacturing autogenous vaccines for poultry in addition to the relevant regulatory considerations. The results from a survey of several European Union member states regarding specific provisions within their national legislations are also presented.

Resistance and Virulence Surveillance in Escherichia coli Isolated from Commercial Meat Samples: A One Health Approach

Escherichia coli is a key indicator of food hygiene, and its monitoring in meat samples points to the potential presence of antimicrobial-resistant strains capable of causing infections in humans, encompassing resistance profiles categorized as serious threats by the Centers for Disease Control and Prevention (CDC), such as Extended-Spectrum Beta-Lactamase (ESBL)-a problem with consequences for animal, human, and environmental health. The objective of the present work was to isolate and characterize ESBL-producing E. coli strains from poultry, pork, and beef meat samples, with a characterization of their virulence and antimicrobial resistance profiles. A total of 450 meat samples (150 chicken, 150 beef, and 150 pork) were obtained from supermarkets and subsequently cultured in medium supplemented with cefotaxime. The isolated colonies were characterized biochemically, followed by antibiogram testing using the disk diffusion technique. Further classification involved biofilm formation and the presence of antimicrobial resistance genes (blaCTX-M, AmpC-type, mcr-1, and fosA3), and virulence genes (eaeA, st, bfpA, lt, stx1, stx2, aggR, iss, ompT, hlyF, iutA, iroN, fyuA, cvaC, and hylA). Statistical analysis was performed via the likelihood-ratio test. In total, 168 strains were obtained, with 73% originating from chicken, 22% from pork, and 17% from beef samples. Notably, strains exhibited greater resistance to tetracycline (51%), ciprofloxacin (46%), and fosfomycin (38%), apart from β-lactams. The detection of antimicrobial resistance in food-isolated strains is noteworthy, underscoring the significance of antimicrobial resistance as a global concern. More than 90% of the strains were biofilm producers, and strains carrying many ExPEC genes were more likely to be biofilm formers (OR 2.42), which increases the problem since the microorganisms have a greater chance of environment persistence and genetic exchange. Regarding molecular characterization, bovine samples showed a higher prevalence of blaCTX-M-1 (OR 6.52), while chicken strains were more likely to carry the fosA3 gene (OR 2.43, CI 1.17-5.05) and presented between 6 to 8 ExPEC genes (OR 2.5, CI 1.33-5.01) compared to other meat samples. Concerning diarrheagenic E. coli genes, two strains harbored eae. It is important to highlight these strains, as they exhibited both biofilm-forming capacities and multidrug resistance (MDR), potentially enabling colonization in diverse environments and causing infections. In conclusion, this study underscores the presence of β-lactamase-producing E. coli strains, mainly in poultry samples, compared to beef and pork samples. Furthermore, all meat sample strains exhibited many virulence-associated extraintestinal genes, with some strains harboring diarrheagenic E. coli (DEC) genes.

Bacteriophage-Associated Antimicrobial Resistance Genes in Avian Pathogenic Escherichia coli Isolated from Brazilian Poultry

Colibacillosis is a disease caused by Escherichia coli and remains a major concern in poultry production, as it leads to significant economic losses due to carcass condemnation and clinical symptoms. The development of antimicrobial resistance is a growing problem of worldwide concern. Lysogenic bacteriophages are effective vectors for acquiring and disseminating antibiotic resistance genes (ARGs). The aim of this study was to investigate the complete genome of Escherichia coli isolates from the femurs of Brazilian broiler chickens in order to investigate the presence of antimicrobial resistance genes associated with bacteriophages. Samples were collected between August and November 2021 from broiler batches from six Brazilian states. Through whole genome sequencing (WGS), data obtained were analyzed for the presence of antimicrobial resistance genes. Antimicrobial resistance genes against the aminoglycosides class were detected in 79.36% of the isolates; 74.6% had predicted sulfonamides resistance genes, 63.49% had predicted resistance genes against β-lactams, and 49.2% of the isolates had at least one of the tetracycline resistance genes. Among the detected genes, 27 have been described in previous studies and associated with bacteriophages. The findings of this study highlight the role of bacteriophages in the dissemination of ARGs in the poultry industry.

The genetic network underlying the evolution of pathogenicity in avian Escherichia coli

Introduction

Colibacillosis is a worldwide prevalent disease in poultry production linked to Escherichia coli strains that belong to the avian pathogenic E. coli (APEC) pathotype. While many virulence factors have been linked to APEC isolates, no single gene or set of genes has been found to be exclusively associated with the pathotype. Moreover, a comprehensive description of the biological processes linked to APEC pathogenicity is currently lacking.

Methods

In this study, we compiled a dataset of 2015 high-quality avian E. coli genomes from pathogenic and commensal isolates, based on publications from 2000 to 2021. We then conducted a genome-wide association study (GWAS) and integrated candidate gene identification with available protein-protein interaction data to decipher the genetic network underlying the biological processes connected to APEC pathogenicity.

Results

Our GWAS identified variations in gene content for 13 genes and SNPs in 3 different genes associated with APEC isolates, suggesting both gene-level and SNP-level variations contribute to APEC pathogenicity. Integrating protein-protein interaction data, we found that 15 of these genes clustered in the same genetic network, suggesting the pathogenicity of APEC might be due to the interplay of different regulated pathways. We also found novel candidate genes including an uncharacterized multi-pass membrane protein (yciC) and the outer membrane porin (ompD) as linked to APEC isolates.

Discussion

Our findings suggest that convergent pathways related to nutrient uptake from host cells and defense from host immune system play a major role in APEC pathogenicity. In addition, the dataset curated in this study represents a comprehensive historical genomic collection of avian E. coli isolates and constitutes a valuable resource for their comparative genomics investigations.

Survey of clinical and commensal Escherichia coli from commercial broilers and turkeys, with emphasis on high-risk clones using APECTyper

Molecular characterization of avian pathogenic Escherichia coli (APEC) is challenging due to the complex nature of its associated disease, colibacillosis, in poultry. Numerous efforts have been made toward defining APEC, and it is becoming clear that certain clonal backgrounds are predictive of an avian E. coli isolate's virulence potential. Thus, APEC can be further differentiated as high-risk APEC based upon their clonal background's virulence potential. However, less clear is the degree of overlap between clinical isolates of differing bird type, and between clinical and gastrointestinal isolates. This study aimed to determine genomic similarities and differences between such populations, comparing commercial broiler vs. turkey isolates, and clinical vs. gastrointestinal isolates. Differences were observed in Clermont phylogenetic groups between isolate populations, with B2 as the dominant group in turkey clinical isolates and G as the dominant group in broiler clinical isolates. Nearly all clinical isolates were classified as APEC using a traditional gene-based typing scheme, whereas 53.4% and 44.1% of broiler and turkey gastrointestinal isolates were classified as APEC, respectively. High-risk APEC were identified among 31.0% and 46.9% of broiler and turkey clinical isolates, compared with 5.7% and 2.9% of broiler and turkey gastrointestinal isolates. As found in previous studies, no specific known virulence or fitness gene sets were identified which universally differentiate between clinical and gastrointestinal isolates. This study further demonstrates the utility of a hybrid APEC typing approach, considering both plasmid content and clonal background, for the identification of dominant and highly virulent APEC clones in poultry production.

Identification and characterization of microRNAs, especially gga-miR-181b-5p, in chicken macrophages associated with avian pathogenic E. coli infection

AbstractAvian pathogenic E. coli (APEC) is a common pathogen in the poultry industry, which can cause substantial economic losses. Recently, emerging evidence showed that the miRNAs were involved in various viral and bacterial infection. To elucidate the role of miRNAs in chicken macrophages in response to APEC infection, we attempted to investigate the miRNAs expression pattern upon APEC infection via miRNA-seq, and to identify the molecular mechanism of the important miRNAs by using RT-qPCR, Western blotting, dual-luciferase reporter assay, and CCK-8. Results showed that a total of 80 differentially expressed (DE) miRNAs were identified in the comparison of APEC vs. wild type group, which corresponded to 724 target genes. Moreover, the target genes of the identified DE miRNAs were mainly significantly enriched in MAPK signaling pathway, Autophagy-animal, mTOR signaling pathway, ErbB signaling pathway, Wnt signaling pathway, TGF-beta signaling pathway. Remarkably, gga-miR-181b-5p is capable to participate in host immune and inflammatory response against APEC infection via targeting of TGFBR1 to modulate the activation of TGF-beta signaling pathway. Collectively, this study provides a perspective of miRNA expression pattern in chicken macrophages upon APEC infection. These findings provide the insight into miRNAs against APEC infection and gga-miR-181b-5p might be a potential target for treating APEC infection.

A molecular epidemiological study on Escherichia coli in young chicks with colibacillosis identified two possible outbreaks across farms

Avian pathogenic Escherichia coli (APEC) is the cause of colibacillosis outbreaks in young poultry chicks, resulting in acute to peracute death. The high morbidity and mortality caused by colibacillosis results in poor animal welfare, reduced sustainability and economical loss worldwide. To advance the understanding of the molecular epidemiology, genomic relatedness and virulence traits of APEC, we performed systematic sampling from 45 confirmed colibacillosis broiler flocks with high first week mortality (FWM) during 2018-2021. From these flocks, 219 APEC isolates were whole genome sequenced (WGS) and bioinformatic analyses were performed. The bioinformatic analyses included sequence typing (ST), serotyping, detection of virulence-associated genes (VAGs) and phylogenetic analysis. Our results showed a high prevalence of ST23, ST429 and ST95 among APEC isolates from Norwegian broiler flocks, and identified ST23, ST429, ST117 and ST371 to cause disease more often alone, compared to ST95, ST69 and ST10. Phylogenetic analyses, together with associated metadata, identified two distinct outbreaks of colibacillosis across farms caused by ST429 and ST23 and gave insight into expected SNP distances within and between flocks identified with the same ST. Further, our results highlighted the need for combining two typing methods, such as serotyping and sequence typing, to better discriminate strains of APEC. Ultimately, systematic sampling of APEC from multiple birds in a flock, together with WGS as a diagnostic tool is important to identify the disease-causing APEC within a flock and to detect outbreaks of colibacillosis across farms.

Assessing the Load, Virulence and Antibiotic-Resistant Traits of ESBL/Ampc E. coli from Broilers Raised on Conventional, Antibiotic-Free, and Organic Farms

Poultry is the most likely source of livestock-associated Extended Spectrum Beta-Lactamase (ESBL) and plasmid-mediated AmpC (pAmpC)-producing E. coli (EC) for humans. We tested the hypothesis that farming methods have an impact on the load of ESBL/pAmpC-EC in the gut of broilers at slaughter. Isolates (n = 156) of antibiotic-free (AF), organic (O), and conventional (C) animals were characterized for antibiotic susceptibility and antibiotic resistance genes. Thirteen isolates were whole-genome sequenced. The average loads of ESBL/pAmpC-EC in cecal contents were 4.17 Log CFU/g for AF; 2.85 Log CFU/g for O; and 3.88 Log CFU/g for C type (p < 0.001). ESBL/pAmpC-EC isolates showed resistance to antibiotic classes historically used in poultry, including penicillins, tetracyclines, quinolones, and sulfonamides. Isolates from O and AF farms harbored a lower proportion of resistance to antibiotics than isolates from C farms. Among the determinants for ESBL/pAmpC, CTX-M-1 prevailed (42.7%), followed by TEM-type (29%) and SHV (19.8%). Avian pathogenic E. coli (APEC), belonging to ST117 and ST349, were identified in the collection. These data confirm the possible role of a broiler as an ESBL/AmpC EC and APEC reservoir for humans. Overall, our study suggests that antibiotic-free and organic production may contribute to a reduced exposure to ESBL/AmpC EC for the consumer.