Virulence factors of Escherichia coli serotypes associated with avian colisepticaemia

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

Pathogenic strains of Escherichia coli infecting poultry, commonly called avian pathogenic E. coli (APEC) present significant risks, to the health of both poultry and the general public. This systematic review aimed to examine the prevalence of APEC serotypes, sequence types (ST), phylogenetic groups, virulence factors and antibiotic resistance patterns based on 189 research papers sourced from PubMed, Web of Science, and ProQuest. Then, data were extracted from the selected studies and analyzed to assess the global distribution and characteristics of APEC strains. The metaprop codes in the Meta and Metafor packages of R as implemented in RStudio were then used to conduct meta-analysis. Among APEC strains identified from these different research reports serogroup O78 had the highest overall prevalence (16 %), followed by serogroups O2 (10 %), and O117 (8 %). The most common ST profiles were ST117 (20 %), ST140 (15 %), ST95 (12 %), and ST131 (9 %). ST117 and ST140 are known reservoirs for pathogenic E. coli in humans. Moreover, phylogenetic assessment highlighted the prevalence of phylogroups A, A1, F, D, and B2 among APEC strains indicating diversity in phylogenetic origin within poultry populations. The presence of antimicrobial resistance was notable among APEC strains against antibiotics such as tetracyclines, penicillins, and cephalosporins. This resistance may be linked to use of antimicrobials in poultry production in certain regions presenting challenges for both animal health management and human infection control. Analysis of sequences linked to adherence or virulence indicated that genes encoding adhesins (csg, fimC), iron/metal uptake (sitB, sitC, iroD) and cytotoxicity (estB, hlyF), and serum resistance (traT, iss) were highly prevalent. These factors have been reported to contribute to APEC host colonization and virulence in poultry. In summary, this overview of the characteristics of APEC highlights the pressing importance of monitoring and implementing management approaches to reduce antimicrobial resistance considering that a phylogenetic diversity of E. coli strains causes infections in both poultry and humans and represents a risk to both animal and public health. Further, determining the major conserved aspects and predominant mechanisms of virulence of APEC is critical for improving diagnostics and developing preventative measures to reduce the burden of infection caused by pathogenic E. coli in poultry and lower risks associated with foodborne transmission of E. coli to humans through poultry and poultry products.

Molecular detection of avian pathogenic Escherichia coli (APEC) in broiler meat from retail meat shop

Avian pathogenic Escherichia coli (APEC) is a major bacterial pathogen responsible for the most widespread form of colibacillosis, resulting in substantial economic losses within the poultry sector and posing a potential public health risk. From July to September 2021, our study investigated the antibiotic resistance pattern of Escherichia coli (E. coli) and the presence of virulence-associated genes (iucD, iutA, iss, and ompT) linked to APEC using 105 broiler meat samples comprising liver, thigh, and breast muscle, in Chitwan, Nepal. E. coli was isolated and identified by culturing samples on MacConkey's agar, Eosin-methylene blue (EMB) agar and performing different biochemical tests. Antibiotic resistance patterns of E. coli were determined by the Kirby-Bauer disc diffusion method. Following the isolation of E. coli, the molecular detection of APEC was performed using conventional polymerase chain reaction (PCR). Out of the 105 samples analyzed, 61 (58.1 %) tested positive for E. coli. In antibiotic susceptibility test (AST), gentamicin and tetracycline exhibited the highest resistance rates, with 90.2 % and 67.2 %, respectively and 29.5 % of the E. coli isolates displayed multidrug-drug resistance. Out of 61 confirmed E. coli isolates, iutA was detected in 47 (77.0 %) samples, iucD in 46 (75.4 %), iss in 53 (86.8 %), and ompT in 39 (63.9 %) samples. This study reports the occurrence of MDR E. coli in meat samples, together with virulence genes associated with APEC which poses a public health threat. Continuous surveillance is vital for monitoring APEC transmission within poultry farms, coupled with efforts to raise awareness of food safety among consumers of broiler meat.

Virulence-associated genes in faecal and clinical Escherichia coli isolates cultured from broiler chickens in Australia

A healthy chicken's intestinal flora harbours a rich reservoir of Escherichia coli as part of the commensal microbiota. However, some strains, known as avian pathogenic E. coli (APEC), carry specific virulence genes (VGs) that enable them to invade and cause extraintestinal infections such as avian colibacillosis. Although several VG combinations have been identified, the pathogenic mechanisms associated with APEC are ill-defined. The current study screened a subset of 88 E. coli isolates selected from 237 pre-existing isolates obtained from commercial poultry flocks in Australia. The 88 isolates were selected based on their enterobacterial repetitive intergenic consensus (ERIC) and antimicrobial resistance (AMR) profiles and included 29 E. coli isolates cultured from chickens with colibacillosis (referred to as clinical E. coli or CEC) and 59 faecal E. coli (FEC) isolates cultured from clinically healthy chickens. The isolates were screened for the presence of 35 previously reported VGs. Of these, 34 were identified, with iucA not being detected. VGs focG, hlyA and sfa/foc were only detected in FEC isolates. Eight VGs had a prevalence of 90% or above in the CEC isolates. Specifically, astA (100%); feoB (96.6%); iutA, iss, ompT, iroN and hlyF (all 93.1%); and vat (89.7%). The prevalence of these were significantly lower in FEC isolates (astA 79.7%, feoB 77.9%, iutA 52.5%, iss 45.8%, ompT 50.9%, iroN 37.3%, hlyF 50.9% and vat 42.4%). The odds ratios that each of these eight VGs were more likely to be associated with CEC than FEC ranged from 7.8 to 21.9. These eight VGs may be used to better define APEC and diagnostically detect APEC in Australia. Further investigations are needed to identify the roles of these VGs in pathogenicity.

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.

Surveillance of Avian Metapneumovirus in Non-Vaccinated Chickens and Co-Infection with Avian Pathogenic Escherichia coli

Brazil is the second largest producer of broiler chicken in the world, and the surveillance of avian pathogens is of great importance for the global economy and nutrition. Avian metapneumovirus (aMPV) infection results in high rates of animal carcass losses due to aerosacculitis and these impacts can be worsened through co-infection with pathogenic bacteria, particularly Escherichia coli (APEC). The present study evaluated the seroprevalence of the main aMPV subtypes in unvaccinated broiler chickens from poultry farms in Brazil, as well as the clinical effects of co-infection with APEC. Blood samples, respiratory swabs, femurs, liver, and spleen of post-mortem broiler chickens were collected from 100 poultry production batches, totaling 1000 samples. The selection of the production batch was based on the history of systemic and respiratory clinical signs. The results indicated that 20% of the lots showed serological evidence of the presence of aMPV, with two lots being positive for aMPV-B. A total of 45% of batches demonstrated co-infection between aMPV and APEC. The results point to the need for viral surveillance, targeted vaccination, and vaccination programs, which could reduce clinical problems and consequently reduce the use of antibiotics to treat bacterial co-infections.

The Isolation and Characterization of Bacteriophages Infecting Avian Pathogenic Escherichia coli O1, O2 and O78 Strains

Avian pathogenic Escherichia coli (APEC), such as O1, O2 and O78, are important serogroups relating to chicken health, being responsible for colibacillosis. In this study, we isolated and characterized bacteriophages (phages) from hen feces and human sewage in Alberta with the potential for controlling colibacillosis in laying hens. The lytic profile, host range, pH tolerance and morphology of seven APEC-infecting phages (ASO1A, ASO1B, ASO2A, ASO78A, ASO2B, AVIO78A and ASO78B) were assessed using a microplate phage virulence assay and transmission electron microscopy (TEM). The potential safety of phages at the genome level was predicted using AMRFinderPlus and the Virulence Factor Database. Finally, phage genera and genetic relatedness with other known phages from the NCBI GenBank database were inferred using the virus intergenomic distance calculator and single gene-based phylogenetic trees. The seven APEC-infecting phages preferentially lysed APEC strains in this study, with ECL21443 (O2) being the most susceptible to phages (n = 5). ASO78A had the broadest host range, lysing all tested strains (n = 5) except ECL20885 (O1). Phages were viable at a pH of 2.5 or 3.5-9.0 after 4 h of incubation. Based on TEM, phages were classed as myovirus, siphovirus and podovirus. No genes associated with virulence, antimicrobial resistance or lysogeny were detected in phage genomes. Comparative genomic analysis placed six of the seven phages in five genera: Felixounavirus (ASO1A and ASO1B), Phapecoctavirus (ASO2A), Tequatrovirus (ASO78A), Kayfunavirus (ASO2B) and Sashavirus (AVIO78A). Based on the nucleotide intergenomic similarity (<70%), phage ASO78B was not assigned a genus in the siphovirus and could represent a new genus in class Caudoviricetes. The tail fiber protein phylogeny revealed variations within APEC-infecting phages and closely related phages. Diverse APEC-infecting phages harbored in the environment demonstrate the potential to control colibacillosis in poultry.

Antimicrobial Efficacy of Cinnamon Essential Oil against Avian Pathogenic Escherichia coli from Poultry

Colibacillosis, caused by E. coli, is responsible for economic losses in the poultry industry due to mortality, decreased production, and the cost of antibiotic treatments. Prevention of colibacillosis is based on improved biosecurity measures and the use of the vaccine performed with O78 E. coli strains, which is responsible for most cases of colibacillosis. Recently, there has been increased interest in other infection control methods, such as the use of natural compounds. The aim of this study was to evaluate the antimicrobial efficacy of cinnamon essential oil (CEO) against E. coli strains isolated from poultry. The MIC50 and MIC90 of CEO were determined by testing 117 strains belonging to serogroups O78, O2, O128, O139, isolated from laying hens (91 strains), broilers (10 strains), and turkeys (16 strains). The bacterial strains were tested at cell densities of 108 and 106 CFU/mL. At the cell density of 108 CFU/mL, MIC50 and MIC90 were 0.4 and 0.5 µL/mL for most of the tested strains, while they corresponded to 0.5 µL/mL for all strains isolated from broilers and for strains belonging to serogroup O139. At the cell density of 106 CFU/mL, MIC50 and MIC90 were 0.3 and 0.4 µL/mL, regardless of bird species of origin and for strains belonging to serogroups O78 and O2. In addition, a concentration of 0.04 µL/mL of CEO corresponded both to MIC50 and MIC90 for strains belonging to serogroups O139 and O128. Based on these results, cinnamon essential oil showed an effective antibacterial activity against E. coli strains from poultry and could find field application for the prevention of colibacillosis.

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.

High resistance of fluoroquinolone and macrolide reported in avian pathogenic Escherichia coli isolates from the humid subtropical regions of Pakistan

OBJECTIVES

This study aimed to assess the antimicrobial resistance profile, virulence potential, and genetic characterization of avian pathogenic Escherichia coli (APEC) that cause colibacillosis in poultry.

METHODS

Antibiotic susceptibility testing (AST) was measured via the Kirby-Bauer disc diffusion method against 27 commonly used antibiotics. Phylogrouping, virulence-associated gene detection, and hybrid strain detection via multiplex polymerase chain reaction (PCR) and genetic diversity were analysed via ERIC-PCR fingertyping method.

RESULTS

AST analysis showed 100% of isolates were multidrug-resistant (MDR) and highest resistance was against penicillin, tetracycline, and macrolide classes of antibiotics. The mcr-1 gene was present in 40% of the isolates, though only 4% of isolates were showing phenotypic resistance. Despite the scarce use of fluoroquinolone, carbapenem, and cephalosporin in the poultry sector, resistance was evident because of the high prevalence of extended-spectrum β-lactamase (ESBL) (53.7%) and other β-lactamases in APEC isolates. β-lactamase genotyping of APEC isolates revealed that 85.7% of isolates contained either blaCTX or blaTEM and around 38% of isolates were complement resistant. Growth in human urine was evident in 67.3% of isolates. Phylogroup B1 (51%) was the most prevalent group followed by phylogroups A (30.6%), D (13.61%), and B2 (4.76%). The most prevalent virulence-associated genes were fimH, iss, and tatT. Results showed that 26 isolates (17.69%) can be termed hybrid strains and APEC/EHEC (enterohemorrhagic E. coli) was the most prevalent hybrid E. coli pathotype. ERIC-PCR fingerprinting genotype analysis clustered APEC isolates in 40 groups (E1-E40). This study provides insights into the antibiotic resistance and virulence profiling of the APEC isolates in Pakistan.

CONCLUSIONS

The findings of this study provide insights into that the antibiotic resistance and virulence profiling of the APEC isolates in Pakistan. This data can inform future studies designed to better estimate the severity of the colibacillosis in poultry farms.

Identification of Subunits for Novel Universal Vaccines against Three Predominant Serogroups and the Emerging O145 among Avian Pathogenic Escherichia coli by Pan-RV Pipeline

Avian pathogenic Escherichia coli, a causative agent of avian colibacillosis, has been causing serious economic losses in the poultry industry. The increase in multidrug-resistant isolates and the complexity of the serotypes of this pathogen, especially the recently reported emergence of a newly predominant serogroup of O145, make the control of this disease difficult. To address this challenge, a high-throughput screening approach, called Pan-RV (Reverse vaccinology based on pangenome analysis), is proposed to search for universal protective antigens against the three traditional serogroups and the newly emerged O145. Using this approach, a total of 61 proteins regarded as probable antigens against the four important serogroups were screened from the core genome of 127 Avian pathogenic Escherichia coli (APEC) genomes, and six were verified by Western blots using antisera. Overall, our research will provide a foundation for the development of an APEC subunit vaccine against avian colibacillosis. Given the exponential growth of whole-genome sequencing (WGS) data, our Pan-RV pipeline will make screening of bacterial vaccine candidates inexpensive, rapid, and efficient. IMPORTANCE With the emergence of drug resistance and the newly predominant serogroup O145, the control of Avian pathogenic Escherichia coli is facing a serious challenge; an efficient immunological method is urgently needed. Here, for the first time, we propose a high-throughput screening approach to search for universal protective antigens against the three traditional serogroups and the newly emerged O145. Importantly, using this approach, a total of 61 proteins regarded as probable antigens against the four important serogroups were screened, and three were shown to be immunoreactive with all antisera (covering the four serogroups), thereby providing a foundation for the development of APEC subunit vaccines against avian colibacillosis. Further, our Pan-RV pipeline will provide immunological control strategies for pathogens with complex and variable genetic backgrounds such as Escherichia coli and will make screening of bacterial vaccine candidates more inexpensive, rapid, and efficient.

Genomic diversity, pathogenicity and antimicrobial resistance of Escherichia coli isolated from poultry in the southern United States

Escherichia coli (E. coli) are typically present as commensal bacteria in the gastro-intestinal tract of most animals including poultry species, but some avian pathogenic E. coli (APEC) strains can cause localized and even systematic infections in domestic poultry. Emergence and re-emergence of antimicrobial resistant isolates (AMR) constrain antibiotics usage in poultry production, and development of an effective vaccination program remains one of the primary options in E. coli disease prevention and control for domestic poultry. Thus, understanding genetic and pathogenic diversity of the enzootic E. coli isolates, particularly APEC, in poultry farms is the key to designing an optimal vaccine candidate and to developing an effective vaccination program. This study explored the genomic and pathogenic diversity among E. coli isolates in southern United States poultry. A total of nine isolates were recovered from sick broilers from Mississippi, and one from Georgia, with epidemiological variations among clinical signs, type of housing, and bird age. The genomes of these isolates were sequenced by using both Illumina short-reads and Oxford Nanopore long-reads, and our comparative analyses suggested data from both platforms were highly consistent. The 16 s rRNA based phylogenetic analyses showed that the 10 bacteria strains are genetically closer to each other than those in the public database. However, whole genome analyses showed that these 10 isolates encoded a diverse set of reported virulence and AMR genes, belonging to at least nine O:H serotypes, and are genetically clustered with at least five different groups of E. coli isolates reported by other states in the United States. Despite the small sample size, this study suggested that there was a large extent of genomic and serological diversity among E. coli isolates in southern United States poultry. A large-scale comprehensive study is needed to understand the overall genomic diversity and the associated virulence, and such a study will be important to develop a broadly protective E. coli vaccine.

Influence of Huangqin Decoction on the immune function and fecal microbiome of chicks after experimental infection with Escherichia coli O78

Huangqin Decoction (HQD), a traditional Chinese medicine formula from the Shang Han Lun written by Zhang Zhongjing, has been used in China for nearly two thousand years. According to the traditional Chinese medicine and previous literature, HQD has the effect of clearing heat, removing toxins, relieving diarrhea and pain. Therefore, HQD was used to prevent or cure many diseases, such as inflammation, diarrhea, malaria, and other acute or chronic gastrointestinal diseases. The effect of HQD, one-herb-absent HQD treatments and enrofloxacin (ENR) on the average daily gain (ADG), mortality rates, visceral index and toll-like receptors (TLRs), inflammatory factors and intestinal microflora in E. coli O78-inoculated chicks were investigated. HQD supplementation increased ADG and reduced the mortality rates caused by E. coli challenge, decreased the heart, liver, bursa of Fabricius (BF) and spleen index. HQD supplementation decreased the serum lysozyme (LZM), IL-1β, TNF-α, IL-10, IL-6 level, down-regulated the mRNA expression of TLR4, -5 and -15 in the spleen by E. coli challenged chicks, and up-regulated the mRNA expression of TLR4, -5 and -15 in BF. At the phylum level, HQD supplementation reversed the increase of Operational Taxonomic Unit (OTUs), decreased the relative abundance of harmful bacteria Proteobacteria, increased the relative abundance of probiotic bacteria Bacteroidetes and Firmicutes. At the genus level, HQD decreased the relative abundance of harmful bacteria Escherichia-Shigella and Pseudomonas. It means that HQD treatment reversed the change of the gut microbiota structure. Compared with HQD, HQD-DZ and HQD-HQ increased the mortality rates. HQD-HQ decreased the ADG and liver index. HQD-GC decreased the spleen index. All herb-absent increased the serum IL-6, but only the HQD-HQ and HQD-SY increased the serum TNF-α. All herb-absent did not activate the TLRs signaling pathways in spleen and BF of chicks. The harmful bacteria Escherichia-Shigella were increased in HQD-HQ and HQD-DZ treatments. HQD-DZ treatment also increased the level of Proteobacteria. The results showed that dietary supplementation with HQD, by down-regulating the mRNA expression of TLR4, -5 and -15 in the spleen, further decreasing the serum LZM and IL-1β, TNF-α, IL-10, IL-6 level, improves the immune function and reverses the change of fecal microbiome in chicks challenged with E. coli. In herb-absent supplementation, the results showed that SY and DZ play a key role in reducing the levels of inflammatory factors and keeping fecal microbiome balance respectively. More importantly, HQ is indispensable in HQD, not only play a key role in reducing the level of inflammatory factors, but also in keeping the balance of fecal microflora.

The Fis Nucleoid Protein Negatively Regulates the Phase Variation fimS Switch of the Type 1 Pilus Operon in Enteropathogenic Escherichia coli

In Escherichia coli the expression of type 1 pili (T1P) is determined by the site-specific inversion of the fimS ON–OFF switch located immediately upstream of major fimbrial subunit gene fimA. Here we investigated the role of virulence (Ler, GrlR, and GrlA) and global regulators (H-NS, IHF, and Fis) in the regulation of the fimS switch in the human enteropathogenic E. coli (EPEC) O127:H6 strain E2348/69. This strain does not produce detectable T1P and PCR analysis of the fimS switch confirmed that it is locked in the OFF orientation. Among the regulator mutants analyzed, only the ∆fis mutant produced significantly high levels of T1P on its surface and yielded high titers of agglutination of guinea pig erythrocytes. Expression analysis of the fimA, fimB, and fimE promoters using lacZ transcriptional fusions indicated that only PfimA activity is enhanced in the absence of Fis. Collectively, these data demonstrate that Fis is a negative regulator of T1P expression in EPEC and suggest that it is required for the FimE-dependent inversion of the fimS switch from the ON-to-OFF direction. It is possible that a similar mechanism of T1P regulation exists in other intestinal and extra-intestinal pathogenic classes of E. coli.

Investigation of Serotype Prevalence of Escherichia coli Strains Isolated from Layer Poultry in Greece and Interactions with Other Infectious Agents

Colibacillosis is the most common bacterial disease in poultry and it is caused by avian pathogenic Escherichia coli (APEC), which is assigned to various O-serogroups. Previous studies have shown that APEC strains are more often related to certain O-serogroups such asO78, O2 and O1. E. coli has been reported to act either as a primary or secondary agent in complicating other infections. The aim of this study was to investigate the occurrence of and characterize the O-serogroups of E. coli strains isolated from commercial layer and layer breeder flocks showing macroscopic lesions of colibacillosis and increased or normal mortality in Greece. Furthermore, we attempted to assess the interaction between infectious agents such as Mycoplasma gallisepticum (MG), Mycoplasma synoviae (MS), infectious bronchitis (IBV) and infectious laryngotracheitis (ILT) with E. coli infections in layer flocks with increased mortality. Our study revealed that in addition to the common serogroups (O78, O2), many other, and less common serogroups were identified, including O111. The O78, O111 and O2 serogroups were frequently detected in flocks with lesions of colibacillosis and increased mortality whereas O2, O88 and O8 were reported more commonly in birds with colibacillosis lesions but normal mortality rates. These data provide important information for colibacillosis monitoring and define preventative measures, especially by using effective vaccination programs because E. coli vaccines are reported to mainly offer homologous protection. Finally, concerning the association of the four tested infectious agents with E. coli mortality, our study did not reveal a statistically significant effect of the above infectious agents tested with E. coli infection mortality.

Increased microbial diversity and decreased prevalence of common pathogens in the gut microbiomes of wild turkeys compared to domestic turkeys

Turkeys (Meleagris gallopavo) provide a globally important source of protein and constitute the second most important source of poultry meat in the world. Bacterial diseases are common in commercial poultry production causing significant production losses for farmers. Due to the increasingly recognized problems associated with large-scale/indiscriminant antibiotic use in agricultural settings, poultry producers need alternative methods to control common bacterial pathogens. In this study we compared the cecal microbiota of wild and domestic turkeys, hypothesizing that environmental pressures faced by wild birds may select for a disease-resistant microbial community. Sequence analysis of 16S rRNA genes amplified from cecal samples indicate that free-roaming wild turkeys carry a rich and variable microbiota compared to domestic turkeys raised on large-scale poultry farms. Wild turkeys also had very low levels of Staphylococcus, Salmonella and E. coli when compared to domestic turkeys. E. coli strains isolated from wild or domestic turkey cecal samples also belong to distinct phylogenetic backgrounds and differ in their propensity to carry virulence genes. E. coli strains isolated from factory-raised turkeys were far more likely to carry genes for capsule (kpsII, kpsIII) or siderophore (iroN, fyuA) synthesis than those isolated from wild turkeys. These results suggest that the microbiota of wild turkeys may provide colonization resistance against common poultry pathogens. Importance Due to the increasingly recognized problems associated with antibiotic use in agricultural settings, poultry producers need alternative methods to control common bacterial pathogens. In this study we compare the microbiota of wild and domestic turkeys. Results suggest that free ranging wild turkeys carry a distinct microbiome when compared to farm raised turkeys. The microbiome of wild birds contains very low levels of poultry pathogens compared to farm raised birds. The microbiomes of wild turkeys may be used to guide development of new ways to control disease in large scale poultry production.

What Flips the Switch? Signals and Stress Regulating Extraintestinal Pathogenic Escherichia coli Type 1 Fimbriae (Pili)

Pathogens are exposed to a multitude of harmful conditions imposed by the environment of the host. Bacterial responses against these stresses are pivotal for successful host colonization and pathogenesis. In the case of many E. coli strains, type 1 fimbriae (pili) are an important colonization factor that can contribute to diseases such as urinary tract infections and neonatal meningitis. Production of type 1 fimbriae in E. coli is dependent on an invertible promoter element, fimS, which serves as a phase variation switch determining whether or not a bacterial cell will produce type 1 fimbriae. In this review, we present aspects of signaling and stress involved in mediating regulation of type 1 fimbriae in extraintestinal E. coli; in particular, how certain regulatory mechanisms, some of which are linked to stress response, can influence production of fimbriae and influence bacterial colonization and infection. We suggest that regulation of type 1 fimbriae is potentially linked to environmental stress responses, providing a perspective for how environmental cues in the host and bacterial stress response during infection both play an important role in regulating extraintestinal pathogenic E. coli colonization and virulence.

The Escherichia coli type III secretion system 2 Is involved in the biofilm formation and virulence of avian Pathogenic Escherichia coli

The Escherichia coli type III secretion system 2 (ETT2) is found in most pathogenic E. coli strains. Although many ETT2 gene clusters carry multiple genetic mutations or deletions, ETT2 is known to be involved in bacterial virulence. To date, no studies have been conducted on the role of ETT2 in the virulence of avian pathogenic Escherichia coli (APEC), which harbours ETT2. Thus, we deleted the ETT2 of APEC strain and evaluated the phenotypes and pathogenicities of the mutant. The results showed that deletion of ETT2 had no effect on APEC growth, but significantly promoted biofilm formation. In addition, as compared to the wild-type （WT） strain, the ETT2 deletion significantly promoted adherence to and invasion of DF-1 chicken fibroblasts and facilitated survival in the sera of specific-pathogen-free chickens. Analysis of the role of ETT2 in animal infection models demonstrated that the distribution of viable bacteria in the blood and organs of chicks infected with the ΔETT2 was significantly higher than those infected with WT. The results of RNA sequencing indicated that multiple genes involved in biofilm formation, lipopolysaccharide components, fimbrial genes and virulence effector proteins are regulated by ETT2. Collectively, these results implicated ETT2 is involved in the biofilm formation and pathogenicity of APEC.

The ETT2 transcriptional regulator EivF affects the serum resistance and pathogenicity of avian pathogenic Escherichia coli

Avian pathogenic Escherichia coli (APEC), a pathotype of extraintestinal pathogenic Escherichia coli (ExPEC), can cause serious systemic infectious diseases in poultry. Escherichia coli type III secretion system 2 (ETT2) is widely distributed in E. coli strains, including ExPEC and Enterohemorrhagic Escherichia coli (EHEC). The transcriptional regulator EivF, which is located at the ETT2 cluster, affects the secretion of LEE-encoded proteins and increases bacterial adhesion to human intestinal epithelial cells in EHEC O157:H7. In a previous study, we demonstrated the transcriptional regulator can affect APEC's motility and biofilm formation. Here, we evaluated whether EivF is involved in the pathogenicity of APEC, and we found that inactivation of eivF significantly enhanced resistance to the serum, adherence to chicken embryo fibroblast (DF-1) cells, and the colonization ability of APEC in chicks. To further clarify the regulation mechanism of transcriptional regulator EivF, we performed transcriptome sequencing to analyze the differentially expressed genes and pathways, showing that EivF regulates membrane, adhesion, environmental stress, and secretion protein genes, and EivF is involved in the localization, biological adhesion, biological regulation, membrane, and toxin activity. These findings indicated that the ETT2 transcriptional regulator EivF plays a crucial role in the pathogenicity of APEC as a negative repressor.

Flagellar rotor protein FliG is involved in the virulence of avian pathogenic Escherichia coli

Avian pathogenic Escherichia coli (APEC), a type of extraintestinal pathogenic E. coli, causes avian colibacillosis, a disease of significant economic importance to poultry producers worldwide, which is characterized by systemic infection. However, the pathogenesis of avian pathogenic E. coli strains is not well defined. Here, the role of a flagellar rotor protein encoded by the fliG gene of avian pathogenic E. coli strain AE17 was investigated. To study the role of FliG in the pathogenicity of APEC, fliG mutant and complemented strains were constructed and characterized. The inactivation of fliG had no effect on APEC growth, but significantly reduced bacterial motility. Compared with the wild type, the fliG mutant was highly attenuated in a chick infection model and showed severe defects in its adherence to and invasion of chicken embryo fibroblast DF-1 cells. The fliG mutant also showed reduced resistance to serum in chicks. The expression of the inflammatory cytokines interleukin 1β (IL1β), IL6, and IL8 was reduced in HD-11 macrophages infected with the fliG mutant strain compared with their expression in the wild-type strain. These results demonstrate that the FliG contributes to the virulence of APEC.

The role of Escherichia coli type III secretion system 2 chaperone protein ygeG in pathogenesis of avian pathogenic Escherichia coli

The Escherichia coli type III secretion system 2 (ETT2) is present in most E. coli strains, carries a 29.9-kb ETT2 pathogenicity island (PAI) and is involved in the virulence of avian pathogenic Escherichia coli (APEC). A chaperone protein is essential for the bacterial secretion system, but the function of the ETT2 chaperone protein has not been determined. This study showed that ygeG had sequence homology with the identified bacterial chaperone protein and it possessed tetratri-copeptide repeats (TPR) containing protein. To investigate the role of ygeG in the ETT2 of APEC, ygeG mutant and complemented strains were constructed and characterized. Inactivation of ygeG had no effect on APEC growth, but significantly promoted biofilm formation, and the adherence to and invasion of DF-1 cells, especially the survival abilities in specific-pathogen-free (SPF) chicken sera serum. Analysis of the role of ygeG in chicken infection models revealed that the deletion of ygeG increased bacterial virulence. RNA Sequencing (RNA-Seq) analyses comparing the APEC wild type and the ygeG mutant indicated that multiple genes encoding biofilm formation, outer membrane proteins, fimbrial genes and virulence effector protein genes were regulated by ygeG. These results revealed the role of ygeG as a chaperone protein that affected the virulence and pathogenicity of APEC.

The Avian Pathogenic Escherichia coli (APEC) pathotype is comprised of multiple distinct, independent genotypes

Avian Pathogenic E. coli (APEC) is the causative agent of avian colibacillosis, resulting in economic losses to the poultry industry through morbidity, mortality and carcass condemnation, and impacts the welfare of poultry. Colibacillosis remains a complex disease to manage, hampered by diagnostic and classification strategies for E. coli that are inadequate for defining APEC. However, increased accessibility of whole genome sequencing (WGS) technology has enabled phylogenetic approaches to be applied to the classification of E. coli and genomic characterization of the most common APEC serotypes associated with colibacillosis O1, O2 and O78. These approaches have demonstrated that the O78 serotype is representative of two distinct APEC lineages, ST-23 in phylogroup C and ST-117 in phylogroup G. The O1 and O2 serotypes belong to a third lineage comprised of three sub-populations in phylogroup B2; ST-95, ST-140 and ST-428/ST-429. The frequency with which these genotypes are associated with colibacillosis implicates them as the predominant APEC populations and distinct from those causing incidental or opportunistic infections. The fact that these are disparate clusters from multiple phylogroups suggests that these lineages may have become adapted to the poultry niche independently. WGS studies have highlighted the limitations of traditional APEC classification and can now provide a path towards a robust and more meaningful definition of the APEC pathotype. Future studies should focus on characterizing individual APEC populations in detail and using this information to develop improved diagnostics and interventions.

Ways to minimize bacterial infections, with special reference to Escherichia coli, to cope with the first-week mortality in chicks: an updated overview

On the commercial level, the poultry industry strives to find new techniques to combat bird's infection. During the first week, mortality rate increases in birds because of several bacterial infections of about ten bacterial species, especially colisepticemia. This affects the flock production, uniformity, and suitability for slaughter because of chronic infections. Escherichia coli (E. coli) causes various disease syndromes in poultry, including yolk sac infection (omphalitis), respiratory tract infection, and septicemia. The E. coli infections in the neonatal poultry are being characterized by septicemia. The acute septicemia may cause death, while the subacute form could be characterized through pericarditis, airsacculitis, and perihepatitis. Many E. coli isolates are commonly isolated from commercial broiler chickens as serogroups O₁, O₂, and O₇₈. Although prophylactic antibiotics were used to control mortality associated with bacterial infections of neonatal poultry in the past, the commercial poultry industry is searching for alternatives. This is because of the consumer's demand for reduced antibiotic-resistant bacteria. Despite the vast and rapid development in vaccine technologies against common chicken infectious diseases, no antibiotic alternatives are commercially available to prevent bacterial infections of neonatal chicks. Recent research confirmed the utility of probiotics to improve the health of neonatal poultry. However, probiotics were not efficacious to minimize death and clinical signs associated with neonatal chicks' bacterial infections. This review focuses on the causes of the increased mortality in broiler chicks during the first week of age and the methods used to minimize death.

Genome evolution and the emergence of pathogenicity in avian Escherichia coli

Chickens are the most common birds on Earth and colibacillosis is among the most common diseases affecting them. This major threat to animal welfare and safe sustainable food production is difficult to combat because the etiological agent, avian pathogenic Escherichia coli (APEC), emerges from ubiquitous commensal gut bacteria, with no single virulence gene present in all disease-causing isolates. Here, we address the underlying evolutionary mechanisms of extraintestinal spread and systemic infection in poultry. Combining population scale comparative genomics and pangenome-wide association studies, we compare E. coli from commensal carriage and systemic infections. We identify phylogroup-specific and species-wide genetic elements that are enriched in APEC, including pathogenicity-associated variation in 143 genes that have diverse functions, including genes involved in metabolism, lipopolysaccharide synthesis, heat shock response, antimicrobial resistance and toxicity. We find that horizontal gene transfer spreads pathogenicity elements, allowing divergent clones to cause infection. Finally, a Random Forest model prediction of disease status (carriage vs. disease) identifies pathogenic strains in the emergent ST-117 poultry-associated lineage with 73% accuracy, demonstrating the potential for early identification of emergent APEC in healthy flocks.

Design, development, and evaluation of the efficacy of a nucleic acid-free version of a bacterial ghost candidate vaccine against avian pathogenic E. coli (APEC) O78:K80 serotype

One of the major bacterial infectious diseases in the poultry industry is avian pathogenic Escherichia coli (APEC), which causes colibacillosis in chickens. To develop a novel nucleic acid-free bacterial ghost (BG) vaccine against the O78:K80 serotype of APEC, in this study we constructed a plasmid that harbored E-lysis and S nuclease (SNUC). Following the expression, the O78:K80 bacteria lost all of their cytoplasmic content and nucleic acids by enzymatic digestion. The functionality of these two proteins in the production procedure of bacterial ghosts was confirmed by monitoring the number of colonies, scanning electron microscopy imaging, gel electrophoresis of genomic DNA, and qPCR on the plasmid content of bacterial ghosts. The protective efficacy of the ghost vaccine generated from O78:K80 serotype of APEC was tested in chickens by injection and inhalation routes and compared with that in chickens that received the injection of a killed vaccine. The O78:K80 BG vaccine candidate, used as injection and inhalation, in comparison with the killed vaccine, triggered higher proinflammatory cytokine expression including IL-6, IL-1β, and TNFSF15; a higher level of antibody-dependent humoral (IgY and IgA) and cellular immune responses (IFNγ and lymphocyte proliferation); and lower lesion scores. According to the results of this study, we suggest that the bacterial ghost technology has the potential to be applied for the development of novel vaccines against avian colibacillosis. This technology provides an effective and reliable approach to make multivalent vaccines for more prevalent APEC strains involved in the establishment of this infectious disease in the poultry industry.

Serogrouping, phylotyping, and virulence genotyping of commensal and avian pathogenic Escherichia coli isolated from broilers in Hamedan, Iran

In the present study, 100 Avian-Pathogenic Escherichia coli (APEC) isolates from colibacillosis-suspected broilers and 100 Avian Faecal Escherichia coli (AFEC) isolates from healthy broilers in Iran were examined by PCR for confirmation of their serogroups and phylogenetic background, and their association with ten virulence-associated genes (VAG) including fimC, iutA, chuA, sitA, iss, cvaA/B, hylA, stx1, stx2, and yjaA. Serogroups O78, O1, O2 and O18 were the prominent strains including 54 % of the APEC and 23 % of the AFEC strains. At phylotyping, the majority of APEC strains belonged to phylogenetic group E (22 %) while for the AFEC strains, half of the isolates were not assigned to any group but the predominant phylogroup was E (27 %). Virulence genotyping, revealed that the predominant VAGs were iutA (97 %), fimC (87 %) and iss (84 %) among APEC strains, and fimC (95 %), iss (93 %) and sitA (87 %) in AFEC strains. This is the first time that phylogroup E is described as predominant phylogroup among APEC strains also, this is the first report on the presence of the stx1 gene in APEC strains isolated from broilers in Iran. The results of the present study indicate that VAGs are more prevalent in APEC strains belonging to O2 and O78 serogroups, also phylogroups E and D have more frequency of VAGs than other phylogroups. Therefore, the APEC strains belonging to O2 and O78 serogroups and phylogroups E and D probably have more pathogenicity to broilers.

Transcriptional Regulator YqeI, Locating at ETT2 Locus, Affects the Pathogenicity of Avian Pathogenic Escherichia coli

Simple Summary

Avian pathogenic Escherichia coli (APEC) is the causative agent of colibacillosis, threatening the development of the poultry industry. The study on APEC’s pathogenic mechanism is of great importance. In this study, we investigated the role of YqeI, a transcriptional regulator locating at E. coli type three secretion system 2 in APEC. The transcriptional results revealed that YqeI affected the expression of the genes involving in bacterial localization, locomotion and biological adhesion. A series experiments also demonstrated that the absence of yqeI decreased the bacterial flagella formation ability, motility ability, antiserum bactericidal ability, adhesion ability and colonization ability. Our data suggested that the transcriptional regulator YqeI indeed participates in the pathogenicity of APEC.

Abstract

Avian pathogenic Escherichia coli (APEC) is the leading cause of systemic infections in poultry worldwide and has a hidden threat to public health. Escherichia coli type three secretion system 2 (ETT2), similar to the Salmonella pathogenicity island SPI1, is widely distributed in APEC and associated with virulence. The function of YqeI, which is one of the hypothetical transcriptional regulators locating at the ETT2 locus of APEC, is unknown. In this study, we successfully obtained the mutant strain AE81ΔyqeI of the wild type strain AE81 and performed the transcriptional profiling assays. Additionally, the transcriptional sequencing results revealed that YqeI influenced localization, locomotion and biological adhesion and so on. The transmission electron microscope observation showed that the wild type strain AE81 possessed long curved flagella, whereas the mutant strain AE81ΔyqeI hardly had any. The strain AE81ΔyqeI exhibited lower motility than AE81 after culturing the dilute bacterial suspension on a semisolid medium. It was also found that the survival ability of AE81ΔyqeI weakened significantly when AE81ΔyqeI was cultured with 0%, 10%, 20%, 30%, 40% and 50% SPF serum in PBS, and AE81ΔyqeI had decreased adherence to DF-1 cells compared with AE81 in the bacterial adhesion assay. The bacterial colonization assay indicated that the virulence of AE81ΔyqeI was reduced in the heart, liver, spleen, and lung. These results confirmed that the transcription regulator YqeI is involved in APEC’s pathogenicity, and this study provides clues for future research.

The role of Enterococcus faecalis during co-infection with avian pathogenic Escherichia coli in avian colibacillosis

Enterococcus spp. (ENT) are frequently co-isolated with avian pathogenic E. coli (APEC) from poultry with colibacillosis, a leading cause of flock mortality. Although largely overlooked, ENT may play an active role in these infections. To assess the frequency of ENT co-isolation in colibacillosis, cultures were collected from birds with gross lesions of omphalitis, polyserositis, and septicaemia over a 3-year period from three turkey flocks and three broiler flocks. In birds diagnosed with colibacillosis based on gross findings and isolation of E. coli, ENT were co-isolated with APEC in 35.7% (n = 41/115) of colibacillosis mortality and 3.7% of total mortality (n = 41/1122). Co-isolated APEC and ENT pairs (n = 41) were further characterized using antimicrobial resistance phenotyping and in vitro co-culture assays. E. faecalis (EF) was the most commonly co-isolated species (68% n = 28/41) and tetracycline resistance was the resistance phenotype most commonly found among APEC (51% n = 21/41) and ENT (93% n = 38/41). Under iron-restricted conditions, EF enhanced APEC growth in a proximity-dependent manner and APEC grown in mixed culture with EF exhibited a significant growth and survival advantage (P ≤ 0.01). In an embryo lethality assay, APEC co-infection with EF resulted in decreased survival of broiler embryos compared to mono-infections (P ≤ 0.05). These data demonstrate that EF augmented APEC survival and growth under iron limiting conditions, possibly translating to the increased virulence of APEC in broiler embryos. Thus, ENT co-infections may be a previously unrecognized contributor to colibacillosis-related mortality. Further investigations into the mechanism of this interaction are warranted. RESEARCH HIGHLIGHTS Enterococcus is frequently co-isolated with avian pathogenic E. coli (APEC). Enterococcus faecalis (EF) enhances survival of APEC in iron restricted conditions. EF co-infection increases APEC virulence in broiler embryos.

Hcp2a of type VI secretion system contributes to IL8 and IL1β expression of chicken tracheal epithelium by affecting APEC colonization

Avian pathogenic Escherichia coli (APEC) is an important pathogen that causes avian colibacillosis in poultry. APEC infection can lead to pathological changes in chicken trachea. The type VI secretion system (T6SS) of APEC contribute to the pathogenicity of APEC. However, whether T6SS plays a role in infection of the trachea remains unclear. We constructed mutant strain Δhcp2a by the Red recombination method system. The role of hcp2a (the structural secretion components and secretory protein of the T6SS) in the infection of trachea was investigated. The mutation strain displayed a significant increase in biofilm formation and a decrease in resistance to chicken serum. Moreover, RNA sequencing analyses showed that infection of chicken tracheal epithelium by the mutant strain Δhcp2a induced differential expression of genes. The result also showed that 14 genes (13 genes were downregulated) were enriched in cytokine-cytokine receptor interaction signalling pathway at 12 and 24 h post infection. The mutation Δhcp2a resulted in significant decreases in the bacterial loads in trachea at 6 and 12 h post infection. Real-time PCR analyses showed that the hcp2a mutation downregulated the expression of IL8 and IL1β at mRNA level in chicken tracheal epithelium. Our results indicate that mutation of hcp2a influenced genes expression of the cytokine-cytokine receptor interaction pathway by decreasing APEC colonization in the trachea.

An Assessment of the Level of Protection Against Colibacillosis Conferred by Several Autogenous and/or Commercial Vaccination Programs in Conventional Pullets upon Experimental Challenge

The prevention of avian colibacillosis has historically been investigated through vaccination, with variable outcomes. Commercial live (attenuated) and inactivated vaccines are reported to have limited efficacy in the context of heterologous challenge. Autogenous vaccination, using field isolates, is widely used, but scarcely documented. Different vaccination programs, including a live commercial vaccine and/or an inactivated autogenous vaccine, were compared for three different avian pathogenic Escherichia coli (APEC) strain (serotypes O78, O18 and O111) challenges. On the pullet farm, four groups of conventional pullets received different vaccination protocols. Group A was kept unvaccinated (control group). Group B was vaccinated three times with a live commercial O78 E. coli vaccine (at one day old, 59 and 110 days of age). Group C was immunized twice (at 79 and 110 days) with a three-valence autogenous vaccine (O78, O18 and O111). Group D was vaccinated first with the commercial vaccine (at one day old and 59 days), then with the autogenous vaccine (110 days). Birds were transferred to the experimental facility at 121 days of age and were challenged 10 days later. In each group, 20 birds were challenged with one of the three APEC strains (O78, O18, O111); in total, 80 birds were challenged by the same strains (20 per group). The recorded outcomes were: mortality rate, macroscopic lesion score in target organs and the bacterial recovery of the challenge strain from bone marrow and pooled organs. When challenged with O78 or O111 strains, birds from groups C and D proved to be significantly better protected, in terms of lesion scoring and bacteriological isolation, than those of groups A and B. With the O18 challenge, only birds of group D presented a statistically significant reduction of their lesion score. To the authors’ knowledge, this is the first report on the efficacy of an immunization program in poultry that combines commercial and autogenous vaccines.

Genomic analysis of Escherichia coli strains isolated from diseased chicken in the Czech Republic

Background

Avian pathogenic Escherichia coli (APEC) can cause various extraintestinal infections in poultry, resulting in massive economic losses in poultry industry. In addition, some avian E. coli strains may have zoonotic potential, making poultry a possible source of infection for humans. Due to its extreme genetic diversity, this pathotype remains poorly defined. This study aimed to investigate the diversity of colibacillosis-associated E. coli isolates from Central European countries with a focus on the Czech Republic.

Results

Of 95 clinical isolates subjected to preliminary characterization, 32 were selected for whole-genome sequencing. A multi resistant phenotype was detected in a majority of the sequenced strains with the predominant resistance to β-lactams and quinolones being associated with TEM-type beta-lactamase genes and chromosomal gyrA mutations respectively. The phylogenetic analysis confirmed a great diversity of isolates, that were derived from nearly all phylogenetic groups, with predominace of B2, B1 and C phylogroups. Clusters of closely related isolates within ST23 (phylogroup C) and ST429 (phylogroup B2) indicated a possible local spread of these clones. Besides, the ST429 cluster carried bla_{CMY-2, − 59} genes for AmpC beta-lactamase and isolates of both clusters were generally well-equipped with virulence-associated genes, with considerable differences in distribution of certain virulence-associated genes between phylogenetically distant lineages. Other important and potentially zoonotic APEC STs were detected, incl. ST117, ST354 and ST95, showing several molecular features typical for human ExPEC.

Conclusions

The results support the concept of local spread of virulent APEC clones, as well as of zoonotic potential of specific poultry-associated lineages, and highlight the need to investigate the possible source of these pathogenic strains.

APEC infection affects cytokine-cytokine receptor interaction and cell cycle pathways in chicken trachea

Avian pathogenic Escherichia coli (APEC) can lead to extraintestinal disease in avian species via respiratory tract infection. However, the regulatory mechanism of APEC on the pathogenicity of chicken trachea epithelium remains unknown. In this study, we examined pathological changes in chicken trachea at different infection times (4, 8, 12 and 24 h). The RNA sequencing of APEC infection group and the PBS group (negative control) of chicken trachea epithelium were analysed. Our studies revealed that the oedema, heterophil infiltration and hyperaemia appeared at 8 and 12 h post APEC infection. And the hyperaemia phenomenon and heterophilic granulocyte infiltration disappeared at 24 h post infection. Then RNA sequencing showed many genes were dynamically expressed in the APEC infection group. At 4, 8 and 12 h post infection, the mRNA of differentially expressed genes were enriched by cytokine-cytokine receptor interaction and the toll-like receptor signalling pathway. The cell cycle pathway was enriched at 24 h post infection. Altogether, these findings suggest that APEC infection induces pathological change in the chicken trachea, the mRNA of differentially expressed genes participating in inflammation and hyperplasia signalling pathways. Which not only provide more evidence for regulatory mechanism of APEC on the pathogenicity of chicken trachea epithelium, but also facilitate the effective management of APEC infections in poultry through trachea.

Occurrence of Escherichia coli in captive psittaciformes: antimicrobial susceptibility and virulence genes

Abstract Captive Psittaciformes may harbor Gram-negative bacteria in their digestive tract, mainly due to poor hygienic conditions and confinement. The present study was carried out with the objective of isolating and identifying Escherichia coli in samples collected from Psittaciformes cages in 50 commercial establishments in the metropolitan region of Goiania, with subsequent antimicrobial susceptibility testing and detection of virulence genes. A total of 141 samples of excreta and swab samples from feeders and water bowls were collected, totaling 423 samples. Escherichia coli was isolated from 9.7% (41/423) samples: 12% (17/141) in excreta, 8.5% (12/141) in feed, and 8.5% (12 /141) in waterers. To determine the susceptibility profile of E. coli isolates, resistance to ciprofloxacin 4.9% (2/41), gentamicin 17.0% (7/41), doxycycline 34.1% (14/41), florfenicol 34.1% (14/41), trimethoprim 39.0% (16/41), tetracycline 41.5% (17/41), enrofloxacin 43.9% (18/41), amoxicillin 48.8% (20/41), neomycin 61.0% (25/41), and sulfonamide 90.2% (37/41) was determined. In 20 isolates, resistance was determined at 4 or more antimicrobials, seven of excreta (7/17), five of feed (5/12), and eight of waterers (8/12). One of the isolates from the waterers showed resistance to all antimicrobials. The iss gene was detected in three isolates, the tsh gene in three, the papC gene in two, traT and eae genes were not detected. In this study, it can be concluded that Psittaciformes commercialized as pet are carry E. coli isolates resistant to most commonly used antimicrobials, mainly sulfonamides and neomycin, besides having virulence and serum resistance genes, which highlights the possibility of the to cause disease in humans.

Virulence and antibiotic resistance profile of avian Escherichia coli strains isolated from colibacillosis lesions in central of Algeria

Background and Aim

Avian pathogenic Escherichia coli cause extensive mortality in poultry flocks, leading to extensive economic losses. To date, in Algeria, little information has been available on virulence potential and antibiotics resistance of avian E. coli isolates. Therefore, the aim of this study was the characterization of virulence genes and antibiotic resistance profile of Algerian E. coli strains isolated from diseased broilers.

Materials and Methods

In this study, 43 avian E. coli strains isolated from chicken colibacillosis lesions at different years were analyzed to determine their contents in 10 virulence factors by polymerase chain reaction, antimicrobial susceptibility to 22 antibiotics belonging to six different chemical classes and genomic diversity by pulsed-field gel electrophoresis (PFGE).

Results

Mainly E. coli isolates (58.1%) carried two at six virulence genes and the most frequent virulence gene association detected were ompT (protectin), hlyF (hemolysin) with 55.8% (p<0.001), and iroN, sitA (iron acquisition/uptake systems), and iss (protectin) with 41.8% (p<0.001). Some strains were diagnosed as virulent according to their virulence gene profile. Indeed, 23.25% of the isolates harbored iroN, ompT, hlyF, iss, and sitA combination, 14% ompT, hlyF, and frz_orf4 (sugar metabolism), and 11,6% iroN, hlyF, ompT, iss, iutA (iron acquisition/uptake systems), and frz _orf4. The chicken embryo lethality assay performed on five isolates confirmed the potential virulence of these strains. All isolates submitted to PFGE analysis yielded different genetic profiles, which revealed their diversity. Overall, 97.2% of the isolates were resistant to at least one antibiotic and 53.5% demonstrated multi-antimicrobial resistance to three different antimicrobial classes. The highest resistance levels were against nalidixic acid (83.4%), amoxicillin and ampicillin (83.3%), ticarcillin (80.5%), pipemidic acid (75%), and triméthoprim-sulfamethoxazole (66.6%). For beta-lactam class, the main phenotype observed belonged to broad-spectrum beta-lactamases. However, extended-spectrum beta-lactamase associated with three at six virulence factors was also detected in 13 isolates. Two of them were attested virulent as demonstrated in the embryo lethality test which constitutes a real public threat.

Conclusion

It would be imperative in avian production to discourage misuse while maintaining constant vigilance guidelines and regulations, to limit and rationalize antimicrobial use.

Dietary genistein supplementation improves intestinal mucosal barrier function in Escherichia coli O78-challenged broilers

Genistein has multiple biological activities in both humans and animals. However, a protective effect of genistein on Escherichia coli (E. coli)-induced intestinal mucosal barrier dysfunction remains unknown. In the present study, a total of 288 1-day-old male Arbor Acre broilers fed a corn-soybean basal diet unsupplemented or supplemented with 20 mg genistein/kg diet were subjected to E. coli serotype O78 (10⁸ cfu per bird) infection or equal volume of sodium chloride at 19 days of age. Sera and tissue samples were collected 2 days after E. coli infection. Growth performance, index of immune-related organs, intestinal barrier permeability, protein level of inflammatory cytokines, sIgA, tight junction protein, and mRNA level of apoptotic genes in jejunum were determined. Mortality rate at 7 days post infection was recorded. The results showed that E. coli challenge led to a reduced average daily gain, a decreased thymus index, and bursal index in broilers, an increase of fluorescein isothiocyanate (FITC)-dextran in serum, and a decreased sIgA in jejunum. These effects were abrogated by genistein administration. Western blot results showed that E. coli infection led to increased protein level of claudin-1 and zonula occludens (ZO)-1, which was largely abolished by genistein. Moreover, E. coli infection resulted increased protein level of TNF-α and IL-6, enhanced mRNA level of Bax and caspase-3, as well as decreased mRNA level of Bcl-2 were abrogated by genistein in jujunum of broilers. In conclusion, the results indicate that genistein supplementation improves intestinal mucosal barrier function which is associated with a regulatory effect on tight junction proteins, sIgA, apoptosis, and secretion of inflammatory cytokines in jejunum of E. coli-challenged broilers.

Duck viral infection escalated the incidence of avian pathogenic Escherichia coli in China

Avian pathogenic Escherichia coli (APEC) causes high mortality in poultry flocks and often is complicated with viral infections, leading to large economic losses; however, little information is available on the epidemiological characteristics of this pathogen in ducks. Therefore, a systemic epidemiological investigation was performed on 325 duck farms from 13 provinces in China during the period of 1 April 2016 until 31 March 2018, covering 2 years. A total of 26 APEC strains were isolated from different farms in this study, and analysis showed that all of those isolates carried multiple virulence-associated genes and drug-resistance genes, which led to high pathogenicity (15/26), strong or moderate biofilm formation (24/26) and multidrug-resistant abilities (26/26). On the other hand, coinfection with APEC, H9 avian influenza virus (AIV) and Tembusu virus (TMUV) was very common on those farms (11/26), with APEC and TMUV sharing a similar morbidity peak (from May to September) and susceptibility (60% infections occurred in ducklings); thus, we speculated that the emerging TMUV infection escalated the APEC incidence in ducks. Finally, the data presented in this report enhance the current understanding of the epidemiology of APEC and different viral infections in ducks and provide additional insight into the critical factors that determine their pathogenicity. Meanwhile, the emergence of multidrug-resistant APEC strains and their coinfection with different viruses emphasize that preventive measures against such infections on poultry farms should be implemented immediately.

ECOR phylotyping and determination of virulence genes in Escherichia coli isolates from pathological conditions of broiler chickens in poultry slaughter-houses of southeast of Iran

Avian pathogenic Escherichia coli (APEC) are responsible for wide ranges of extra-intestinal diseases in poultry including colibacillosis, cellulitis, coligranuloma and yolk sac infection. Numbers of virulence are considered important in the pathogenicity of these diseases. The aims of the present study were phylogenetic typing and virulence genes detection in Escherichia coli isolates from colibacillosis and cellulitis of broiler chickens in poultry slaughterhouses of Shahrbabak region, Kerman, Iran. A total number of eighty three E. coli isolates were taken from broiler chickens with colibacillosis and thirty four isolates were taken from carcasses with cellulitis in the industrial slaughterhouses. Biochemically confirmed E. coli isolates were subjected to polymerase chain reaction assay to determine phylogenetic groups and presence of pap C, sfa/focDE, iucD, afaIB-C, hlyA, fimH and crl virulence genes. Colibacillosis isolates were belonged to A (54.21%), B1 (7.22%), B2 (6.03%) and D (32.53%) phylogroups. Whereas, the isolates from cellulitis cases were belonged to three main phylogroups; A (55.88%), B1 (5.88%) and D (38.24%). Statistical analysis showed a specific association between the presence of crl virulence gene and phylogroups of A and D in colibacillosis isolates. The results showed that the isolates from both diseases in broiler chickens could be assigned to various phylogenetic groups (mainly A(. Also, the virulence genes profile of cellulitis E. coli is completely different from that of colibacillosis in this region.

Characteristics of Escherichia coli isolated from broiler chickens with colibacillosis in commercial farms from a common hatchery

To investigate the epidemiologic aspects of colibacillosis in broiler chickens, 83 Escherichia coli isolates obtained from the pericarditis and perihepatitis lesions in broiler chickens from 4 commercial farms, 5 isolates recovered from 5 samples of yolk sac contents that were pooled from 25 emaciated chicks, and 4 fecal isolates obtained from a hatchery that supplied chicks to the 4 commercial farms mentioned above were genetically and bacteriologically characterized. Using pulsed-field gel electrophoresis (PFGE), a total of 92 isolates were classified into 33 pulsotypes. Identical pulsotypes were observed in isolates obtained from hatchery samples and the affected broiler chickens on multiple farms at various sampling times. Seventeen representative isolates with no common origin belonging to 6 pulsotypes and an additional 27 isolates with the other pulsotypes were used for further experiments. Isolates with identical pulsotypes exhibited common traits for virulence-associated genes, lipopolysaccharide core types, and phylogenetic groups. Nine of the isolates were serologically typed as O125 with various types of H antigens and 3 were typed as O25:H4. In the 27 isolates resistant to ceftiofur (CTF), which is a third generation cephalosporin, the blaCTX-M-2, blaCMY-2, blaCTX-M-14, blaCTX-M-65 genes were found in 15, 8, 3, and 1 isolate(s), respectively, and another isolate resistant to CTF had both the blaCTX-M-2 and the blaCMY-2 genes. In the 16 isolates with the blaCTX-M-2 gene, the chromosomal location of the gene was identified in 12 isolates. The plasmid-mediated quinolone resistance genes, oqxAB and aac(6')-Ib-cr, were found in 2 and 3 isolates, respectively. Conjugation experiments revealed that the blaCTX-M-2 (4 isolates), blaCTX-M-14 (3 isolates), blaSHV-12 (1 isolate), and oqxAB (2 isolates) genes were transferred. Our data suggest that E. coli strains with identical pulsotypes had been caused the incidences of colibacillosis and that the antimicrobial resistance genes on conjugative plasmids and those integrated into the chromosome may be spread among avian pathogenic E. coli strains in multiple farms.

A bivalent vaccine derived from attenuated Salmonella expressing O-antigen polysaccharide provides protection against avian pathogenic Escherichia coli O1 and O2 infection

Avian pathogenic Escherichia coli (APEC), a leading cause of avian airsacculitis and colibacillosis, is responsible for significant economic loss in the poultry industry. APEC serogroups O1, O2, and O78 are predominantly associated with disease. Lipopolysaccharide (LPS) O-antigen has been shown to be a potent antigen for inducing specific protective immune responses. Therefore, we sought to develop a multivalent polysaccharide vaccine to prevent most APEC infections. We previously reported the stable expression of plasmid pSS27 encoding the APEC O1 O-antigen gene cluster (10.8 kb) in attenuated Salmonella enterica serovar Typhimurium S740 provided excellent protection against APEC O1 challenge. In this study, the plasmid pSS28 harboring the APEC O2 O-antigen polysaccharide gene cluster (15.5 kb) was constructed. Biosynthesis of pSS28-encoded APEC O2 O-antigen in Salmonella vaccine strain S740 was validated by Western blot. The recombinant Salmonella vaccine strain S740 (pSS28) elicited homologous protection against virulent wild-type APEC O2 challenge in a chicken model. Furthermore, through equal-volume mixing the two monovalent vaccine strains S740 (pSS27) and S740 (pSS28), a bivalent vaccine candidate against both APEC O1 and O2 was developed. Immunization of chickens with the bivalent vaccine elicited production of serum IgG and mucosal sIgA antibodies against the LPS of both APEC O1 and O2. Moreover, antibodies induced by the bivalent vaccine promoted opsonization, provoked complement-mediated bactericidal activity, and elicited protection against lethal challenge with both virulent APEC O1 and O2 strains. These results demonstrate that the bivalent vaccine comprised of S740 (pSS27) and S740 (pSS28) is a promising vaccine candidate against APEC O1 and O2 infection.

Antimicrobial activity of carbon monoxide-releasing molecule [Mn(CO)3(tpa-κ3N)]Br versus multidrug-resistant isolates of Avian Pathogenic Escherichia coli and its synergy with colistin

Antimicrobial resistance is a growing global concern in human and veterinary medicine, with an ever-increasing void in the arsenal of clinicians. Novel classes of compounds including carbon monoxoide-releasing molecules (CORMs), for example the light-activated metal complex [Mn(CO)₃(tpa-κ³N)]Br, could be used as alternatives/to supplement traditional antibacterials. Avian pathogenic Escherichia coli (APEC) represent a large reservoir of antibiotic resistance and can cause serious clinical disease in poultry, with potential as zoonotic pathogens, due to shared serotypes and virulence factors with human pathogenic E. coli. The in vitro activity of [Mn(CO)₃(tpa-κ³N)]Br against multidrug-resistant APECs was assessed via broth microtitre dilution assays and synergy testing with colistin performed using checkerboard and time-kill assays. In vivo antibacterial activity of [Mn(CO)₃(tpa-κ³N)]Br alone and in combination with colistin was determined using the Galleria mellonella wax moth larvae model. Animals were monitored for life/death, melanisation and bacterial numbers enumerated from larval haemolymph. In vitro testing produced relatively high [Mn(CO)₃(tpa-κ³N)]Br minimum inhibitory concentrations (MICs) of 1024 mg/L. However, its activity was significantly increased with the addition of colistin, bringing MICs down to ≤32 mg/L. This synergy was confirmed in time-kill assays. In vivo assays showed that the combination of [Mn(CO)₃(tpa-κ³N)]Br with colistin produced superior bacterial killing and significantly increased larval survival. In both in vitro and in vivo assays light activation was not required for antibacterial activity. This data supports further evaluation of [Mn(CO)₃(tpa-κ³N)]Br as a potential agent for treatment of systemic infections in humans and animals, when used with permeabilising agents such as colistin.

Prevalence of colibacillosis in chickens in greater Mymensingh district of Bangladesh

Aim:

This study was conducted for determination of the prevalence of colibacillosis in chicken in poultry farms in Mymensingh and Tangail districts. Isolation, identification, and antibiogram profile of Escherichia coli were also performed.

Materials and Methods:

A total of 25 chickens manifested clinical signs of colibacillosis were collected from five different poultry farms during natural outbreaks.

Results:

In broiler, the prevalence of colibacillosis was 0.84%, and in layer, prevalence was 0.80%. The prevalence of colibacillosis was 1.0% and 0.5% in 25-30 days old and 31-35 days old broiler, respectively. In case of layer birds, the prevalence was 0.6% in 40-45 days old bird and 1% in 46-50 days old bird. Identity of the E. coli isolate of chicken was confirmed by sugar fermentation, biochemical tests, and polymerase chain reaction assay. Antibiogram profile of E. coli isolate of chicken revealed that it was multidrug resistant (resistant against two antibiotics, such as ampicillin and cefalexin).

Conclusion:

Data of this study suggest that colibacillosis is prevalent in the study areas which underscore the need of implementation of prevention and control measure against this disease.

Escherichia coli Type III Secretion System 2 ATPase EivC Is Involved in the Motility and Virulence of Avian Pathogenic Escherichia coli

Type III secretion systems (T3SSs) are crucial for bacterial infections because they deliver effector proteins into host cells. The Escherichia coli type III secretion system 2 (ETT2) is present in the majority of E. coli strains, and although it is degenerate, ETT2 regulates bacterial virulence. An ATPase is essential for T3SS secretion, but the function of the ETT2 ATPase has not been demonstrated. Here, we show that EivC is homologous to the β subunit of F0F1 ATPases and it possesses ATPase activity. To investigate the effects of ETT2 ATPase EivC on the phenotype and virulence of avian pathogenic Escherichia coli (APEC), eivC mutant and complemented strains were constructed and characterized. Inactivation of eivC led to impaired flagella production and augmented fimbriae on the bacterial surface, and, consequently, reduced bacterial motility. In addition, the eivC mutant strain exhibited attenuated virulence in ducks, diminished serum resistance, reduced survival in macrophage cells and in ducks, upregulated fimbrial gene expression, and downregulated flagellar and virulence gene expression. The expression of the inflammatory cytokines interleukin (IL)-1β and IL-8 were increased in HD-11 macrophages infected with the eivC mutant strain, compared with the wild-type strain. These virulence-related phenotypes were restored by genetic complementation. These findings demonstrate that ETT2 ATPase EivC is involved in the motility and pathogenicity of APEC.

DNA microarray-mediated transcriptional profiling of avian pathogenic Escherichia coli O2 strain E058 during its infection of chicken

Avian pathogenic Escherichia coli (APEC) cause typical extraintestinal infections in poultry, including acute fatal septicemia, subacute pericarditis, and airsacculitis. These bacteria most often infect chickens, turkeys, ducks, and other avian species, and therefore pose a significant economic burden on the poultry industry worldwide. Few studies have analyzed the genome-wide transcriptional profile of APEC during infection in vivo. In this study, we examined the genome-wide transcriptional response of APEC O2 strain E058 in an in vivo chicken infection model to better understand the factors necessary for APEC colonization, growth, and survival in vivo. An Affymetrix multigenome DNA microarray, which contains most of the genomic open reading frames of E. coli K-12 strain MG1655, uropathogenic E. coli strain CFT073, and E. coli O157:H7 strain EDL 933, was used to profile the gene expression in APEC E058. We identified the in vivo transcriptional response of APEC E058 bacteria collected directly from the blood of infected chickens. Significant differences in expression levels were detected between the in vivo expression profile and the in vitro expression profile in LB medium. The genes highly expressed during infection were involved in metabolism, iron acquisition or transport, virulence, response to stress, and biological regulation. The reliability of the microarray data was confirmed by performing quantitative real-time PCR on 12 representative genes. Moreover, several significantly upregulated genes, including yjiY, sodA, phoB and spy, were selected to study their role in APEC pathogenesis. The data will help to better understand the mechanisms of APEC pathogenesis.

Diversity of Escherichia coli strains involved in vertebral osteomyelitis and arthritis in broilers in Brazil

BACKGROUND

Locomotor disorders and infections by Escherichia coli represent major concerns to the poultry industry worldwide. Avian pathogenic E. coli (APEC) is associated with extraintestinal infections leading to respiratory or systemic disease known as colibacillosis. The most common lesions seen in cases of colibacillosis are perihepatitis, airsacculitis, pericarditis, peritonitis/salpingitis and arthritis. These diseases are responsible for significant economic losses in the poultry industry worldwide. E. coli has been recently isolated from vertebral osteomyelitis cases in Brazil and there are no data on molecular and phenotypic characteristics of E. coli strains isolated from lesions in the locomotor system of broilers. This raised the question whether specific E. coli strains could be responsible for bone lesions in broilers. The aim of this study was to assess these characteristics of E. coli strains isolated from broilers presenting vertebral osteomyelitis and arthritis in Brazil.

RESULTS

Fifteen E. coli strains from bone lesions were submitted to APEC diagnosis and setting of ECOR phylogenic group, O serogroup, flagella type, virulence genes content, genetic patterns by Pulsed Field Gel Electrophoresis (PFGE) and Multilocus Sequence Typing (MLST). In addition, bacterial isolates were further characterized through a lethality test, serum resistance test and antibiotic resistance profile. E. coli strains harbored different genetic pattern as assessed by PFGE, regardless of flock origin and lesion site. The strains belonged to seven sequence types (STs) previously described (ST117, ST101, ST131, ST 371 and ST3107) or newly described in this study (ST5766 and ST5856). ECOR group D (66.7 %) was the most frequently detected. The strains belonged to diverse serogroups (O88, O25, O12, and O45), some of worldwide importance. The antibiotic resistance profile confirmed strains' diversity and revealed a high proportion of multidrug-resistant strains (73 %), mainly to quinolones and beta-lactams, including third generation cephalosporin. The percentage of resistance to tetracycline was moderate (33 %) but always associated with multidrug resistance.

CONCLUSIONS

Our results demonstrated that vertebral osteomyelitis and arthritis in broilers can be associated with highly diverse E. coli based on molecular and phenotypic characteristics. There was no specific virulence patterns of the E. coli strains associated with vertebral osteomyelitis or arthritis. Also, E. coli strains were frequently multidrug resistant and belonged to STs commonly shared by APEC and human ExPEC strains.

Comparison between avian pathogenic (APEC) and avian faecal (AFEC) Escherichia coli isolated from different regions in Brazil

Detection and analysis of virulence-associated genes (VAGs) of avian pathogenic Escherichia coli (APEC) may be helpful to distinguish pathogenic from commensal faecal strains (AFEC). The aim of this study was to characterise 120 isolates of avian Escherichia coli, comprising 91 APEC (from diseased birds) and 29 AFEC (from healthy chickens), collected in Brazil. Phylogenetic analysis and in vivo pathogenicity testing was performed on 38 VAGs. The VAGs iucD, iutA, iroN, fepC, ompT, cvi and hlyF were statistically associated with medium and high pathogenicity (MP/HP) strains. A minimal group of seven VAGs may be required to accurately discriminate pathogenic and non-pathogenic avian strains of E. coli in Brazil.

The virulence factor ychO has a pleiotropic action in an Avian Pathogenic Escherichia coli (APEC) strain

Background

Avian pathogenic Escherichia coli strains cause extraintestinal diseases in birds, leading to substantial economic losses to the poultry industry worldwide. Bacteria that invade cells can overcome the host humoral immune response, resulting in a higher pathogenicity potential. Invasins are members of a large family of outer membrane proteins that allow pathogen invasion into host cells by interacting with specific receptors on the cell surface.

Results

An in silico analysis of the genome of a septicemic APEC strain (SEPT362) demonstrated the presence of a putative invasin homologous to the ychO gene from E. coli str. K-12 substr. MG1655. In vitro and in vivo assays comparing a mutant strain carrying a null mutation of this gene, a complemented strain, and its counterpart wild-type strain showed that ychO plays a role in the pathogenicity of APEC strain SEPT362. In vitro assays demonstrated that the mutant strain exhibited significant decreases in bacterial adhesiveness and invasiveness in chicken cells and biofilm formation. In vivo assay indicated a decrease in pathogenicity of the mutant strain. Moreover, transcriptome analysis demonstrated that the ychO deletion affected the expression of 426 genes. Among the altered genes, 93.66 % were downregulated in the mutant, including membrane proteins and metabolism genes.

Conclusion

The results led us to propose that gene ychO contributes to the pathogenicity of APEC strain SEPT362 influencing, in a pleiotropic manner, many biological characteristics, such as adhesion and invasion of in vitro cultured cells, biofilm formation and motility, which could be due to the possible membrane location of this protein. All of these results suggest that the absence of gene ychO would influence the virulence of the APEC strain herein studied.

Genetic Characterization of ExPEC-Like Virulence Plasmids among a Subset of NMEC

Neonatal Meningitis Escherichia coli (NMEC) is one of the most common causes of neonatal bacterial meningitis in the US and elsewhere resulting in mortality or neurologic deficits in survivors. Large plasmids have been shown experimentally to increase the virulence of NMEC in the rat model of neonatal meningitis. Here, 9 ExPEC-like plasmids were isolated from NMEC and sequenced to identify the core and accessory plasmid genes of ExPEC-like virulence plasmids in NMEC and create an expanded plasmid phylogeny. Results showed sequenced virulence plasmids carry a strongly conserved core of genes with predicted functions in five distinct categories including: virulence, metabolism, plasmid stability, mobile elements, and unknown genes. The major functions of virulence-associated and plasmid core genes serve to increase in vivo fitness by adding multiple iron uptake systems to the genetic repertoire to facilitate NMEC’s survival in the host’s low iron environment, and systems to enhance bacterial resistance to host innate immunity. Phylogenetic analysis based on these core plasmid genes showed that at least two lineages of ExPEC-like plasmids could be discerned. Further, virulence plasmids from Avian Pathogenic E. coli and NMEC plasmids could not be differentiated based solely on the genes of the core plasmid genome.