Longitudinal study of transmission of Escherichia coli from broiler breeders to broilers

A systematic review on the role of biosecurity to prevent or control colibacillosis in broiler production

This systematic review aimed at investigating the role that biosecurity can have in preventing or controlling colibacillosis in broiler production. Primary studies with natural or experimental exposure to avian pathogenic Escherichia coli, evaluating any biosecurity measure to prevent or control colibacillosis in broiler chickens with at least one of the following outcomes: feed conversion ratio (FCR), condemnations at slaughter, and mortality due to colibacillosis, were included. A systematic search was carried out in 4 databases according to the Cochrane handbook and reported following the PRISMA 2020 directions. Studies (n = 3,886) were screened in a 2-phase process and data matching the inclusion criteria were extracted. Risk of bias assessment was performed. Four studies reporting biosecurity measures to prevent or control colibacillosis in broiler production were included. In all studies, only disinfection during either the pre-hatching period (n = 3) or the post-hatching period (n = 1) was evaluated as biosecurity measure in broiler production, as well as its effect on FCR (n = 2) and mortality (n = 4) due to colibacillosis. No studies with effects on condemnations at slaughter were found. Due to the heterogeneity of studies in regard to interventions and outcomes, meta-analysis was not carried out. The limited findings of this systematic review do not provide a comprehensive evidence to statistically evaluate the efficacy of biosecurity to prevent or control colibacillosis in broiler production. The scarcity of evidence found suggests that further and deeper investigations on the topic are needed, considering the variety of interventions related to biosecurity.

Persistence of commensal multidrug-resistant Escherichia coli in the broiler production pyramid is best explained by strain recirculation from the rearing environment

Despite the success of mitigation policies in several countries to reduce the use of antibiotics in veterinary medicine, pathogenic and commensal bacteria resistant to antibiotics are still circulating in livestock animals. However, factors contributing the most to antimicrobial resistance (AMR) persistence in these settings are yet not clearly identified. The broiler production, with its highly segmented, pyramidal structure offers an ideal context to understand and control the spread of resistant bacteria. By taking advantage of an experimental facility reproducing the whole broiler production pyramid, we demonstrate that resistant E. coli persist in our system primarily though recirculation of a few commensal clones surviving in the rearing environment. No vertical transmission from hens to offspring nor strain acquisition at the hatchery were detected, while import of new strains from outside the facility seems limited. Moreover, each clone carries its own resistance-conferring plasmid(s), and a single putative plasmid horizontal transfer could have been inferred. These results, observed for now in a small experimental facility with high level of biosecurity, must be confirmed in a commercial farm context but still provide invaluable information for future mitigation policies.

Characterization of Escherichia coli pathogenicity and drug resistance in yolk peritonitis

Yolk Peritonitis can lead to a rapid decline in egg production, which seriously affects the health of laying hens and the profitability of chicken farms. Escherichia coli (E. coli) is the most common cause of yolk peritonitis in laying hens. In this study, bacterial samples were collected from the ovaries and fallopian tubes of laying hens with suspected yolk peritonitis from a laying farm in Jiangsu Province, and their pathogenicity and drug resistance were investigated. Initially, morphological and biochemical detection methods were employed to isolate and identify the pathogenic bacteria. The results showed that a total of 16 strains of E. coli were isolated from laying hens with yolk peritonitis. Subsequently, the drug resistance and pathogenicity of a randomly selected E. coli strain were analyzed and predicted by genome sequencing technology, and the drug resistance of E. coli was verified by drug sensitivity test and PCR. Finally, the virulence was verified by infection experiment in mice. The study revealed that the egg-yolk peritonitis in laying hens was caused by E. coli infection, and the genome sequencing analysis revealed that the bacteria had multidrug resistance and high virulence. The drug susceptibility testing indicates that E. coli exhibited resistance to aminoglycosides, β-lactam, macrolides, fluoroquinolones, and sulfonamides. In this study, resistance genes including KdpE, aadA5, APH(3 ")-ID, APH(6)-ID, and TEM-1 were identified, and their expression levels varied across different stages of bacterial growth. The results of virulence analysis indicated a mortality rate of 50% in mice infected with E. coli at a concentration of 2.985 × 107 CFU/mL. E. coli infection resulted in damage to various tissues and organs in mice, with the intestinal tissue structure being the most severely affected. This study provides a reference for the study of drug resistance mechanisms in E. coli and provides valuable insights into the selection of drugs for the treatment of vitelline peritonitis.

Molecular epidemiology, antibiotic resistance profile and frequency of integron 1 and 2 in adherent-invasive Escherichia coli isolates of colorectal cancer patients

This study explores the prevalence of adherent-invasive Escherichia coli (AIEC) in colorectal cancer (CRC) patients and investigates the potential of effective intracellular antibiotics as a therapeutic strategy for CRC patients with AIEC infections. Considering the pivotal role of integrons in bacterial antibiotic resistance, the frequency of class 1 and 2 integrons in AIEC isolated from CRC patients, in one of the referenced 3 gastroenterology clinics in Isfahan, Iran was examined. AIEC strains were isolated from the colorectal biopsies and their antimicrobial sensitivity was assessed using the disc diffusion method. Polymerase chain reaction (PCR) was employed to detect intl1 and intl2. The multilocus sequence typing (MLST) method was utilized to type 10 selected isolates. Of the 150 samples, 24 were identified as AIEC, with the highest number isolated from CRC2 (33.4%) and CRC1 (29.16%), and the least from the FH group (8.3%) and control group (12.5%). int1 in 79.2% and int2 in 45.8% of AIEC strains were found and 41.6% of strains had both integrons. AIEC isolates with int1 exhibited the highest sensitivity to trimethoprim-sulfamethoxazole (57.9%), while those with int2 showed the highest sensitivity to ciprofloxacin (63.6%). A significant association between resistance to rifampin and integron 2 presence in AIEC isolates was observed. Furthermore, a significant correlation between integron 1 presence, invasion, survival, and replication within macrophages in AIEC strains was identified. MLST analysis revealed ST131 from CC131 with integron 1 as the most common sequence type (ST). The emergence of such strains in CRC populations poses a serious public health threat. The distribution pattern of STs varied among studied groups, with pandemic STs highlighting the importance of examining and treating patients infected with these isolates. Comprehensive prospective clinical investigations are warranted to assess the prognostic value of detecting this pathovar in CRC and to evaluate therapeutic techniques targeting drug-resistant AIECs, such as phage therapy, bacteriocins, and anti-adhesion compounds, for CRC prevention and treatment.

Re-evaluating efficacy of vaccines against highly pathogenic avian influenza virus in poultry: A systematic review and meta-analysis

The global spread of highly pathogenic avian influenza (HPAI) A (H5N1) clade 2.3.4.4b virus since 2021 necessitates a re-evaluation of the role of vaccination in controlling HPAI outbreaks among poultry, which has been controversial because of the concern of silent spread with viral mutation and spillover to human. We systematically reviewed and meta-analyzed all existing data from experimental challenge trials to assess the efficacy of HPAI vaccines against mortality in specific pathogen free (SPF) chickens, with evaluation of the certainty of evidence (CoE) using the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) approach. Out of 223 screened publications, 46 trials met our eligibility criteria. Inactivated vaccines showed an efficacy of 95% (risk ratio [RR] = 5% [95% CI: 1% to 17%], I2 = 0%, CoE high) against homologous strains and an efficacy of 78% (RR = 22% [95% CI: 14% to 37%], I2 = 18%, CoE high) against heterologous strains (test for subgroup difference p = 0.02). Live recombinant vaccines exhibited the highest efficacy at 97% (RR = 3% [95% CI: 1% to 13%], I2 = 0%, CoE high). Inactivated recombinant vaccines had an overall efficacy of 90% (RR = 10% [95% CI: 6% to 16%], I2 = 47%, CoE high). Commercial vaccines showed an overall efficacy of 91% (RR = 9% [95% CI: 5% to 17%], I2 = 23%, CoE high), with 96% efficacy (RR = 4% [95% CI: 1% to 21%], I2 = 0%, CoE high) against homologous strains and 90% efficacy (RR = 10% [95% CI: 5% to 20%], I2 = 31%, CoE moderate) against heterologous strains. Our systematic review offers an updated and unbiased assessment of vaccine efficacy against HPAI-related mortality, providing timely and crucial information for re-evaluating the role of vaccination in poultry avian influenza control policy amist the global HPAI outbreak post-2021.

Phenotypic virulence characterization of avian pathogenic Escherichia coli (APEC) isolates from broiler breeders with colibacillosis in Mississippi

AIMS

In this study, we evaluated the phenotypic virulence characteristics of avian pathogenic Escherichia coli (APEC) isolates from broiler breeders with colibacillosis in Mississippi. Also, the relationship between phenotypic and genotypic virulence patterns was determined.

METHODS AND RESULTS

Twenty-eight APEC isolated from lesions of broiler breeders diagnosed with colibacillosis were used for embryo lethality assay and chick challenge study. The percentage of embryo mortality following embryo lethality assay and pathogenicity score following the chick challenge study were used to categorize the isolates based on virulence. Pearson correlation analysis was performed to determine the relationship between embryo mortality, chick pathogenicity, and the presence of virulence-associated genes in the isolates. Overall, 39.3% of the isolates were highly virulent and 3.5% were avirulent, following both assays. There existed a positive correlation between embryo mortality and chick pathogenicity (r = 0.73, P < .01), as well as percentage embryo mortality and pathogenicity score with the presence of some virulence genes.

CONCLUSIONS

Even though all the APEC were isolated from lesions of diseased breeders, the virulence potential varied from being avirulent to highly virulent. Further, we identified a positive relationship between phenotypic virulence and the frequency of virulence-associated genes.

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.

Avian Pathogenic Escherichia coli (APEC) in Broiler Breeders: An Overview

Poultry meat is one of the major animal protein sources necessary to meet the global protein demand. Sustainability in broiler production is the key to achieving its continuous supply, and broiler breeders play a critical role in maintaining this sustainability by providing good quality chicks. Colibacillosis, the disease caused by avian pathogenic Escherichia coli (APEC), causes severe economic losses to the poultry industry globally. Moreover, APEC causes an additional burden among broiler breeders, such as a decrease in egg production and mortality among these birds. There is vertical transmission of APEC to the broiler chicks through eggs, resulting in increased first-week mortality and subsequent horizontal transmission at the hatchery. In this regard, the vertical transmission of antibiotic resistance genes is another concern that needs attention. Controlling several diseases in broiler breeders would possibly reduce the first-week mortality in chicks, thereby maintaining the production level. For that, constant monitoring of the bacterial populations is critical. Moreover, amidst the increased antibiotic resistance pattern, more focus on alternative treatment strategies like vaccines, probiotics, and bacteriophages is necessary. Future research focusing on strategies to mitigate APEC in broiler breeders would be one of the finest solutions for sustainable broiler production.

Clonal diversity and zoonotic potential of MDR Escherichia coli isolated from poultry at different age intervals

1. A pool of 480 E. coli isolates of poultry (broilers and ducks) representing different time intervals (0, 10, 20 and 30 days) was selected for ribotyping and used to determine polymorphism of 16-23S ribosomal RNA intergenic space. All the isolates were multidrug-resistant (MDR).2. Out of these, 10 isolates were tested for MultiLocus Sequence Typing (MLST) among which novel allelic combinations and therefore new sequence types were identified in seven isolates.3. This work showed the changes in E. coli strains structure at farm level and individual bird level in host species raised on organised farms with similar parental lineage and environmental housing. The statistical results showed that the structure of variation is very different by farm, supporting a strong effect of location, which confirms the temporal clustering.4. There were significant differences between E. coli strains in chickens and ducks, indicating host specificity of the E. coli strains.5. Some of the pathogenic E. coli strains found using MLST belonged to ST735, ST2796 and a pandemic clone ST752 of ST10 clonal complex. The results strongly suggested the clonal expansion and establishment of specific MDR clones that have zoonotic relevance.

Dramatic increase in slaughter condemnations due to Escherichia coli ST23 and ST101 within the Danish broiler production

Escherichia coli constitutes a major challenge to poultry even when the prevalence of colibacillosis is low. Additionally, specific E. coli strains can severely enhance the detrimental effects on productivity, animal welfare and antimicrobial use. In 2019-2020, a dramatic increase in colibacillosis occurred among Danish broilers causing late-onset mortality and high slaughter condemnations. In the present study, the pathology and causative E. coli-types were characterised. Furthermore, the outbreak-related strains were compared to isolates from concurrent "background" colibacillosis. During the study, 1039 birds were subjected to a comprehensive post-mortem examination, and a total of 349 E. coli isolates were sequenced and characterised by multi-locus sequence typing, virulence and resistance gene presence, plasmid replicon content and phylogenetic analysis. Productivity data from outbreak flocks revealed a mortality of 6.34% ± 3.74 and a condemnation of 5.04% ± 3.67. Contrary, the numbers were 3.18% ± 1.57% and 1.02% ± 0.4 among non-outbreak flocks, respectively. Major lesions were cellulitis (46.82%), airsacculitis (67.63%), pericarditis (55.49%), perihepatitis (41.04%) and femoral head necrosis with physeal/metaphyseal involvement (44.51%). Among non-outbreak broilers, the prevalence was 4.46%, 7.64%, 7.01%, 3.82% and 8.28%, respectively. ST23 and ST101 dominated heavily in outbreak flocks, whereas non-outbreak related isolates consisted of various other STs. A low level of resistance markers was evident, except in few multidrug-resistant isolates. Within ST23 and ST101, 13 and 12 virulence genes were significantly over-represented compared to non-outbreak isolates. In conclusion, clonal lineages were documented as the cause of a devastating outbreak of colibacillosis with great prospects for future interventions.

Prevalence of Potential Pathogenic and Antimicrobial Resistant Escherichia coli in Danish Broilers

Avian pathogenic Escherichia coli (APEC) are important bacteria in broiler production in terms of economy, welfare, and use of antibiotics. During a previous outbreak of APEC in the Nordic countries, it was suggested that the pathogenic clones of E. coli causing the outbreak originated from grandparent stock and were transmitted to the offspring, causing increased first week mortality. This study investigated whether the pathogenic potential of E. coli at the parent and broiler level differs in relation to pathogenic potential described by the level of virulence-associated genes and pattern of antimicrobial resistance. The hypothesis was that, due to higher biosecurity at the parent level, the E. coli population will show a lower level of antimicrobial resistance and carry fewer virulence-associated genes, as a result of fewer E. coli infections observed. From four parent flocks and eight broiler flocks, 715 E. coli were isolated from cloacal swabs of newly hatched chickens (Ross 308). The isolated E. coli were characterized by eight virulence-associated genes and phenotypic resistance against six antimicrobials. It was found that the prevalence of virulence-associated genes and phenotypic antimicrobial resistance varied significantly between flocks, and the virulence-associated genes papC and irp2 and resistance against ampicillin were significantly more prevalent in breeder flocks compared to broiler flocks.

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.

Characterization of Escherichia coli and other bacteria isolated from condemned broilers at a Danish abattoir

Meat inspection is important to ensure food safety and protect public health. Visual inspection of slaughtered carcasses for pathological changes should be supported by bacteriological analysis to determine whether the entire carcass or parts of it should be condemned. The aim of this study was to determine the bacterial species present in different sample types from condemned broiler carcasses. Furthermore, we investigated the genetic characteristics, zoonotic potential, and relatedness of Escherichia coli, the predominant bacterial species isolated from the carcasses. A total of 400 broiler carcasses condemned because of cellulitis (100), scratches (100), hepatitis (100), and healthy control carcasses (100) were selected. Samples of meat, pathological lesion, and bone marrow of each carcass were obtained for microbial analysis. From the analyzed samples, 469 bacterial isolates were recovered with E. coli accounting for 45.8%, followed by Aeromonas spp. (27.9%), in particular A. veronii. The highest rate of bacterial isolation was observed in carcasses condemned with cellulitis, whereas carcasses with hepatitis had the lowest rate of bacterial isolation. Forty-four E. coli isolates originating from different sample types were selected for whole genome sequencing. A clonal relationship was shown between E. coli from different sample types of the same carcass condemned with cellulitis and scratches. A major clade of E. coli was found in carcasses condemned with cellulitis with isolates containing mdf(A), tet(A), and bla TEM-1B genes that confer resistance to macrolides, tetracycline, and ampicillin, respectively. E. coli in this clade all belonged to ST117 and clustered with E. coli isolates previously collected from dead chickens and carcasses condemned due to cellulitis in Denmark, Finland, and the United Kingdom. Bacterial evaluation results of carcasses condemned with cellulitis, scratches (moderate to severe skin lesion), and acute hepatitis confirmed the need for total condemnation of carcasses with these pathological findings. A similar evaluation should be done for carcasses affected with chronic hepatitis, and minor scratches lesions.

Effects of late incubation temperature and moment of first post-hatch feed access on neonatal broiler development, temperature preference, and stress response

Early life experiences are known to be of great importance for later life. For instance, exposure to stress during early life can increase fearfulness at later age. In broilers, delayed feeding after hatch may cause metabolic stress. Besides, delayed feeding after hatch may affect neonatal broiler development and thermogenesis and consequently preferred ambient temperature. Moreover, these effects of feeding strategy may be dependent on late incubation temperature. To study this, eggs (n = 1,338) from a 54-wk-old Ross broiler breeder flock were incubated at 37.8°C (control) or 36.7°C (lower) eggshell temperature (EST) during late incubation (≥ embryonic d 17). At hatch, two feeding strategies were applied (direct access (early feeding) or 51 to 54 h delayed access (delayed feeding)). Broilers (n = 960) were equally divided over 32 pens and grown for 3 wk. Stress was assessed by determination of corticosterone in blood at 0 h, 48 h, 96 h and d 21 after hatch. Fearfulness was assessed by tonic immobility at d 13. Temperature preference was assessed at d 2 and d 12. Broiler development was determined at 0 h, 48 h, and 96 h after hatch. There was no EST × feeding strategy interaction for any parameter (P ≥ 0.07). Early feeding resulted in a 2.5× lower plasma corticosterone concentration at 48 h (P < 0.01) and a 2.2°C and 2.0°C lower preference temperature for d 2 and d 12 respectively (P = 0.01) compared to delayed feeding. Tonic immobility was not affected. In conclusion, early feeding reduces exposure to stress in the short term and stimulates thermoregulatory ability of broilers in the longer term.

Longitudinal study on background lesions in broiler breeder flocks and their progeny, and genomic characterisation of Escherichia coli

In broiler breeders, background mortality is rarely addressed, however, it represents the death of a vast number of birds, a constant productivity loss, welfare concerns and it might affect chick quality. The study aimed to unveil lesions leading to mortality in a study population perceived as healthy, combined with whole-genome sequencing (WGS) of Escherichia coli, a well-known contributor to disease problems in poultry. Broiler breeders (n = 340) originating from three distinct, putative healthy flocks and their progeny (n = 154) were subjected to a comprehensive post-mortem examination, bacteriological sampling, and sequencing of 77 E. coli isolates. Productivity data confirmed an exemplary health status of the enrolled flocks, and post-mortem examination further verified the absence of general disease problems. Among the submitted broiler breeders, exudative peritonitis (31.2%) was the most frequent lesion linked to infectious disease, whereas airsacculitis, pericarditis, perihepatitis, and salpingitis occurred in 18.5%, 3.5%, 3.8% and 17%, respectively. Yolksacculitis occurred in 15.6% of the broilers, whilst pericarditis, perihepatitis and peritonitis were diagnosed in 9.7%, 7.1% and 9.1%, respectively. WGS revealed a diverse population where ST95 dominated the population retrieved from broiler breeders, whereas ST10 was highly prevalent among broilers. Both lineages could be isolated from extraintestinal sites of birds without lesions indicative of infection. In general, the genetic diversity within flocks was comparable to the diversity between farms, and the overall occurrence of resistance markers was low. In conclusion, a comprehensive insight into lesions associated with background mortality is presented, together with a vast diversity of E. coli isolated from extraintestinal sites during a non-outbreak situation.

High-Frequency Detection of fosA3 and bla CTX-M-55 Genes in Escherichia coli From Longitudinal Monitoring in Broiler Chicken Farms

Considering the worrying emergence of multidrug resistance, including in animal husbandry and especially in food-producing animals, the need to detect antimicrobial resistance strains in poultry environments is relevant, mainly considering a One Health approach. Thus, this study aimed to conduct longitudinal monitoring of antimicrobial resistance in broiler chicken farms, with an emphasis on evaluating the frequency of resistance to fosfomycin and β-lactams. Escherichia coli was isolated from broiler chicken farms (cloacal swabs, meconium, poultry feed, water, poultry litter, and Alphitobius diaperinus) in northern Paraná from 2019 to 2020 during three periods: the first period (1st days of life), the second period (20th to 25th days of life), and third period (40th to 42nd days of life). Antibiogram tests and the detection of phenotypic extended-spectrum β-lactamase (ESBL) were performed, and they were confirmed by seaching for genes from the bla_CTX–M group. The other resistance genes searched were mcr-1 and fosA3. Some ESBL bla_CTX–M–1 group strains were selected for ESBL identification by sequencing and enterobacterial repetitive intergenic consensus-polymerase chain reaction analysis. To determine the transferability of the bla_{CTX–M–1–} and fosA3-carrying plasmids, strains were subjected to conjugation experiments. A total of 507 E. coli were analyzed: 360 from cloacal swabs, 24 from meconium samples, 3 from poultry feed samples, 18 from water samples, 69 from poultry litter samples, and 33 from A. diaperinus samples. Among the strain isolate, 80% (406/507) were multidrug-resistant (MDR), and 51% (260/507) were ESBL-positive, with the bla_CTX–M–1 group being the most frequent. For the fosA3 gene, 68% (344/507) of the strains isolated were positive, deserves to be highlighted E. coli isolated from day-old chickens (OR 6.34, CI 2.34–17.17), when compared with strains isolated from other origins (poultry litter, A. diaperinus, water, and poultry feed). This work alerts us to the high frequency of the fosA3 gene correlated with the CTX-M-1 group (OR 3.57, CI 95% 2.7–4.72, p < 0.05), especially the bla_CTX–M–55 gene, in broiler chickens. This profile was observed mainly in day-old chicken, with a high percentage of E. coli that were MDR. The findings emphasize the importance of conducting longitudinal monitoring to detect the primary risk points during poultry production.

Litter Commensal Bacteria Can Limit the Horizontal Gene Transfer of Antimicrobial Resistance to Salmonella in Chickens

Fostering a "balanced" gut microbiome through the administration of beneficial microbes that can competitively exclude pathogens has gained a lot of attention and use in human and animal medicine. However, little is known about how microbes affect the horizontal gene transfer of antimicrobial resistance (AMR). To shed more light on this question, we challenged neonatal broiler chicks raised on reused broiler chicken litter-a complex environment made up of decomposing pine shavings, feces, uric acid, feathers, and feed-with Salmonella enterica serovar Heidelberg (S. Heidelberg), a model pathogen. Neonatal chicks challenged with S. Heidelberg and raised on reused litter were more resistant to S. Heidelberg cecal colonization than chicks grown on fresh litter. Furthermore, chicks grown on reused litter were at a lower risk of colonization with S. Heidelberg strains that encoded AMR on IncI1 plasmids. We used 16S rRNA gene sequencing and shotgun metagenomics to show that the major difference between chicks grown on fresh litter and those grown on reused litter was the microbiome harbored in the litter and ceca. The microbiome of reused litter samples was more uniform and enriched in functional pathways related to the biosynthesis of organic and antimicrobial molecules than that in fresh litter samples. We found that Escherichia coli was the main reservoir of plasmids encoding AMR and that the IncI1 plasmid was maintained at a significantly lower copy per cell in reused litter compared to fresh litter. These findings support the notion that commensal bacteria play an integral role in the horizontal transfer of plasmids encoding AMR to pathogens like Salmonella. IMPORTANCE Antimicrobial resistance spread is a worldwide health challenge, stemming in large part from the ability of microorganisms to share their genetic material through horizontal gene transfer. To address this issue, many countries and international organizations have adopted a One Health approach to curtail the proliferation of antimicrobial-resistant bacteria. This includes the removal and reduction of antibiotics used in food animal production and the development of alternatives to antibiotics. However, there is still a significant knowledge gap in our understanding of how resistance spreads in the absence of antibiotic selection and the role commensal bacteria play in reducing antibiotic resistance transfer. In this study, we show that commensal bacteria play a key role in reducing the horizontal gene transfer of antibiotic resistance to Salmonella, provide the identity of the bacterial species that potentially perform this function in broiler chickens, and also postulate the mechanism involved.

Layers, broiler chickens and their F1 cross develop distinctly different caecal microbial communities when hatched and reared together

Aim

To compare the caecal microbiota of layer, broiler, and intermediate F1 layer × broiler cross birds with the hypothesis that significant differences in caecal microbial composition would persist between the three groups when host and environmental interactions were minimized.

Methods and Results

Caecal contents were characterized using 16S rRNA for males of broiler (n = 12), layer (n = 12) and F1 layer × broiler cross (n = 9) birds that were hatched and reared under the same conditions. The microbial community structure differed significantly between the three groups of birds at phylum, genus and OTU levels, with clear separation of the groups observed. Firmicutes was the phylum most represented across samples; however, the high abundance of Proteobacteria in the layer birds at d28 post‐hatch was unexpected, and driven by a higher abundance of E. coli.

Conclusions

The microbiota phylotype between broilers, layers and their F1 cross significantly differed in community structure, diversity and relative abundance in the absence of environmental confounding, which is generally difficult to avoid in microbial studies.

Significance and Impact of Study

The results provide a unique comparison and evidence that there is a strong genetic component driving microbial composition within poultry strains, despite the embryonic development occurring in ovo.

Feather pulp: a novel substrate useful for proton nuclear magnetic resonance spectroscopy metabolomics and biomarker discovery

Noninvasive biomarkers of stress that are predictive of poultry health are needed. Feather pulp is highly vascularized and represents a potential source of biomarkers that has not been extensively explored. We investigated the feasibility and use of feather pulp for novel biomarker discovery using ¹H-Nuclear Magnetic Resonance Spectroscopy (NMR)-based metabolomics. To this end, high quality NMR metabolomic spectra were obtained from chicken feather pulp extracted using either ultrafiltration (UF) or Bligh-Dyer methanol-chloroform (BD) methods. In total, 121 and 160 metabolites were identified using the UF and BD extraction methods, respectively, with 71 of these common to both methods. The metabolome of feather pulp differed in broiler breeders that were 1-, 23-, and 45-wk-of-age. Moreover, feather pulp was more difficult to obtain from older birds, indicating that age must be considered when targeting feather pulp as a source of biomarkers. The metabolomic profile of feather pulp obtained from 12-day-old broilers administered corticosterone differed from control birds, indicating that the metabolome of feather pulp was sensitive to induced physiological stress. A comparative examination of feather pulp and serum in broilers revealed that the feather pulp metabolome differed from that of serum but provided more information. The study findings show that metabolite biomarkers in chicken feather pulp may allow producers to effectively monitor stress, and to objectively develop and evaluate on-farm mitigations, including practices that reduce stress and enhance bird health.

Occurrence of Colibacillosis in Broilers and Its Relationship With Avian Pathogenic Escherichia coli (APEC) Population Structure and Molecular Characteristics

Avian pathogenic Escherichia coli (APEC) causes colibacillosis, the disease with the highest economic loss for the broiler industry. However, studies focusing on the prevalence and population structure of APEC in the broiler production pyramid are scarce. Here, we used genotyping and serotyping data to elucidate the APEC population structure and its changes in different broiler production stages along with whole-genome sequencing (WGS) in a subset of APEC isolates to determine transmission patterns amongst dominant APEC sequence types (STs) and characterize them in detail. Comparison of genotypes encountered in both APEC and avian fecal E. coli (AFEC) provided further insights. Overall, APEC-related mortality, as the proportion of the total sampled mortality in the broiler production, was high (35%), while phylogroup C and serogroup O78 were predominant amongst APEC isolates. We found a low (34.0%) and high (53.3%) incidence of colibacillosis in chicks and end-cycle broilers, respectively, which may be related to a shift in APEC genotypes, suggesting a trend from commensalism to pathogenicity across different broiler production stages. Despite considerable APEC genotypic diversity, there was substantial genotype overlap (40.9%, overall) over the production stages and convergence of STs to the four clusters. Within these clusters, WGS data provided evidence of clonal transmission events and revealed an enriched virulence and resistance APEC repertoire. More specifically, sequenced APEC were assigned to defined pathotypes based on their virulence gene content while the majority (86%) was genotypically multi-drug resistant. Interestingly, WGS-based phylogeny showed that a subset of APEC, which are cephalosporin-resistant, may originate directly from cephalosporin-resistant AFEC. Finally, exploration of the APEC plasmidome indicated that the small fraction of the APEC virulome carried by IncF plasmids is pivotal for the manifestation of the APEC pathotype; thus, plasmid exchange can promote pathogenicity in strains that are at the edge of the commensal and pathogenic states.

Recovery of probiotic bacteria from the intestinal tract of broilers after noninvasive pre-hatch application

This paper reports the success of intestinal colonisation of chickens and foetuses by probiotics after different methods of pre-hatch application. Hatcheries not using in ovo injection of probiotics or wish to avoid the reduced hatchability associated with in ovo injections prefer using alternatives to in ovo technologies. Therefore, we used noninvasive pre-hatch application methods. This included the vertical transmission of probiotics from the mother hen to offspring, application of probiotic late in incubation and transmission of probiotics during hatch. Enterococcus faecium (NCIMB11181) and Lactobacillus animalis (DSM33570) were used as probiotics. Probiotics were applied either through drinking water for the mother hens, by dipping the eggs in a probiotic solution on days 16-18 of incubation or through drops/spray on the eggshell of the fertilised eggs. Similarly, intestinal colonisation of the probiotic in chickens was investigated either before hatch (pre-hatch) or immediately after hatch (post-hatch). Based on the performed experiments, it is concluded that E. faecium was vertically transmitted from the mother hen to the offspring, as E. faecium was recovered in 20 and 33% of the offspring pre- and post-hatch, respectively. When applied on the eggshell, the recovery of E. faecium before hatch depended on the application method and ranged from 0 to 9%. In contrast, L. animalis was not recovered before hatch. Moreover, when sampling post-hatch 100% of the chickens were colonised when E. faecium was used and 54% were colonised when L. animalis was used. Furthermore, spray application with E. faecium was the most successful application method as 9% of the foetuses were colonised pre-hatch and 100% became colonised post-hatch. Therefore, pre-hatch application by, for example, spray of probiotics on the eggshell can be used as an easy-to-use, noninvasive method for early life colonisation of chicken gut.

Influence of Feeding Omega-3 Polyunsaturated Fatty Acids to Broiler Breeders on Indices of Immunocompetence, Gastrointestinal, and Skeletal Development in Broiler Chickens

Modern broiler chickens are associated with rapid growth rates and superior feed efficiency. However, they are also susceptible to physiological and metabolic disorders (e.g., skin lesions, lameness, sudden death, enteric diseases, myopathies) that exert substantial economic losses to producers. This is further exacerbated by consumer pressure and mandated cessation of production practices such as indiscriminate use of antimicrobial growth promoters. Manipulation of broiler breeder (BB) nutrition and management can influence chick quality, robustness, and resilience to stressors in the production environment. The present review examines the role of feeding BB functional polyunsaturated omega-3 fatty acids (n-3 PUFA) and subsequent impact on the indices of immunocompetence, skeletal, and gastrointestinal (GIT) development in broiler chickens. Research in mammalian and avian models led evidence that perinatal feeding of long chain n-3 PUFA such as eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) engender transgenerational effects through regulation of a variety of biological processes including development of vital organs such as skeleton, brain and GIT. It is shown that feeding poultry breeders n-3 PUFA decreases inflammatory states and enriches hatching eggs with n-3 PUFA and immunoglobulins. Further evidence also shows that after 15 days of incubation, chicken embryos preferentially utilize long chain n-3 PUFA-critical for optimal cell, tissues, and organ development. Enrichment of n-3 PUFA in newly hatchling tissues reduce proinflammatory eicosanoids with consequences of enhanced bone mineralization. Dietary n-3 PUFA also modulates breeder GIT microbiota with consequences of microbial colonization and succession in chicks. As well, research shows that feeding poultry breeders n-3 PUFA bolsters progeny immunocompetence through enhanced passive immunity and antibody titres against routine vaccination. In conclusion, it appears that chicks may benefit from the incorporation of n-3 PUFA in the breeder diets; however, little attention is paid to fatty acids composition in breeder nutrition. We also highlight gaps in knowledge and future research perspectives.

Co-Infection of Escherichia coli, Enterococcus faecalis and Chlamydia psittaci Contributes to Salpingitis of Laying Layers and Breeder Ducks

Salpingitis is manifested as hemorrhagic follicular inflammation exudations and peritonitis, leading to reduced egg production and high culling of breeder flocks. From 2018 to 2021, increasing salpingitis during egg peak is threatening the poultry industry post-artificial insemination, both in breeder layers and breeder ducks across China. In our study, Escherichia coli (E. coli), Enterococcus faecalis(E. faecalis) and Chlamydia psittaci (C. psittaci) were isolated and identified from the diseased oviducts using biochemical tests and PCR. To identify and isolate pathogenicity, we inoculated the isolates into laying hens via an intravaginal route. Later, laying hens developed typical salpingitis after receiving the combination of the aforementioned three isolates (1 × 10⁵ IFU/mL of C. psittaci and 1 × 10⁶ CFU/mL of E. faecalis and E. coli, respectively), while less oviduct inflammation was observed in the layers inoculated with the above isolate alone. Furthermore, 56 breeder ducks were divided into seven groups, eight ducks per group. The birds received the combination of three isolates, synergic infection of E. coli and E. faecalis, and C. psittaci alone via vaginal tract, while the remaining ducks were inoculated with physiological saline as the control group. Egg production was monitored daily and lesions of oviducts and follicles were determined post-infection on day 6. Interestingly, typical salpingitis, degenerated follicles and yolk peritonitis were obviously found in the synergic infection of three isolates and the birds inoculated with C. psittaci alone developed hemorrhagic follicles and white exudates in oviducts, while birds with E. faecalis or E. coli alone did not develop typical salpingitis. Finally, higher E. coli loads were determined in the oviducts as compared to E. faecalis and C. psittaci infection. Taken together, the combination of E. coli and E. faecalis, and C. psittaci could induce typical salpingitis and yolk peritonitis both in laying hens and breeder ducks. Secondary infection of E. coli and E. faecalis via artificial insemination is urgently needed for investigation against salpingitis.

Commensal Escherichia coli Antimicrobial Resistance and Multidrug-Resistance Dynamics during Broiler Growing Period: Commercial vs. Improved Farm Conditions

Simple Summary

This experiment was designed to evaluate the differences in antimicrobial and multidrug resistance dynamics in broilers reared under two different farm conditions (commercial vs. improved) during the growing period, using Escherichia coli as sentinel bacterium. Although no antibiotics were applied during rearing for two different management conditions tested, high rates of antimicrobial and multidrug-resistant bacteria were observed throughout rearing, with the percentages of resistant bacteria observed being of particular concern in day-old chicks on arrival day and in chickens at the end of the growing period, just before delivery to the slaughterhouse.

Abstract

New measures applied to reduce antimicrobial resistances (AMR) at field level in broiler production are focused on improving animals’ welfare and resilience. However, it is necessary to have better knowledge of AMR epidemiology. Thus, the aim of this study was to evaluate AMR and multidrug resistance (MDR) dynamics during the rearing of broilers under commercial (33 kg/m² density and max. 20 ppm ammonia) and improved (17 kg/m² density and max. 10 ppm ammonia) farm conditions. Day-old chicks were housed in two poultry houses (commercial vs. improved), and no antimicrobial agents were administered at any point. Animals were sampled at arrival day, mid-period and at slaughter day. High AMR rates were observed throughout rearing. No statistical differences were observed between groups. Moreover, both groups presented high MDR at slaughter day. These results could be explained by vertical or horizontal resistance acquisition. In conclusion, AMR and MDR are present throughout rearing. Moreover, although a lower level of MDR was observed at mid-period in animals reared under less intensive conditions, no differences were found at the end. In order to reduce the presence of AMR bacteria in poultry, further studies are needed to better understand AMR acquisition and prevalence in differing broiler growing conditions.

Phylogenetic characterization of avian pathogenic Escherichia coli strains longitudinally isolated from broiler breeder flocks vaccinated with autogenous vaccine

Escherichia coli is the most common bacterial cause of infections in poultry farms. It is known for its genetic heterogenicity that complicates the protection of poultry health through immunoprophylaxis. In farms with continuous problems with colibacillosis, autogenous E. coli vaccine was implemented to the vaccination program instead of commercial vaccines. In this study, we investigated the effect of the autogenous vaccine on E. coli phylogroup diversity on 2 broiler breeder farms with 4 and 5 flocks, respectively. The first flocks on both farms were vaccinated with commercial vaccines, while application of autogenous vaccine was introduced in the second flock on both farms. In total, 113 strains were selected based on the target organs and age of chickens. Targeted organs were the peritoneum, liver, oviduct, and bone marrow, and analyzed strains were isolated from chickens older than 21 wk of age when problems with colibacillosis start emerging. The strains were phylotyped by PCR and allocated to phylogroups A, B1, B2, C, D, E, F or clades I–V. The results showed that autogenous vaccine could significantly affect the phylogroup shift of the strains. On farm A, application of the autogenous vaccine induced significantly lower prevalence (P = 0.01) of the phylogroups represented in the vaccine among the strains later isolated from the vaccinated flock, while on farm B, the results showed a decrease in the phylogenetic diversity with a dominant prevalence of group B2 despite the vaccine application. The results indicate that implementation of the autogenous vaccine can repress the majority of the strains, but also be unable to eliminate the presence of certain phylogroups, and thus lead to strain shift. Further detailed analyses of multilocus sequence typing and virulence genes will elucidate the pathogenic potential and selection of certain strains, with emphasis on B2 phylogroup.

New strategies to prevent and control avian pathogenic Escherichia coli (APEC)

Avian pathogenic Escherichia coli (APEC) infections are associated with major economical losses and decreased animal welfare. In broiler production, APEC infections have traditionally been controlled by antibiotics, resulting in an increased prevalence of antibiotic-resistant E. coli. Concerns have been raised that transfer of antibiotic-resistant APEC via the food chain may result in risks for extra-intestinal infection of humans related to zoonotic transfer and increased difficulties in the treatment of human infections caused APEC-related E. coli types. In this review, the risks associated with APEC are presented based on new knowledge on transmission, virulence and antibiotic resistance of APEC. A major new change in our understanding of APEC is the high degree of genuine vertical transfer of APEC from parents to offspring. A new strategy for controlling APEC, including control of antibiotic-resistant APEC, has to focus on limiting vertical transfer from parents to offspring, and subsequent horizontal transmission within and between flocks and farms, by using all-in-all-out production systems and implementing a high level of biosecurity. Vaccination and the use of competitive exclusion are important tools to be considered. A specific reduction of antibiotic-resistant APEC can be obtained by implementing culling strategies, only allowing the use of antibiotics in cases where animal welfare is threatened. Strategies to reduce APEC, including antibiotic-resistant APEC, need to be implemented in the whole production pyramid, but it has to start at the very top of the production pyramid.

Longitudinal monitoring of multidrug resistance in Escherichia coli on broiler chicken fattening farms in Shandong, China

The extensive use of antibiotics has, in recent years, caused antimicrobial resistance and multidrug resistance in Escherichia coli to gradually develop into a worldwide problem. These resistant E. coli could be transmitted to humans through animal products and animal feces in the environment, thereby creating a problem for bacterial treatment for humans and animals and resulting in a public health issue. Monitoring the resistance of E. coli throughout the broiler fattening period is therefore of great significance for both the poultry industry and public health. In this longitudinal study, samples were taken from 6 conventional broiler fattening farms in Shandong Province, China, at 3 different times within 1 fattening period. The overall isolation rate of E. coli was 53.04% (375/707). Antibiotic resistance was very common in the E. coli isolated from these farms, and differed for different antibiotics, with ampicillin having the highest rate (92.86%) and cefoxitin the lowest (10.12%). Multidrug resistance was as high as 91.07%. More importantly, both the resistance rate of E. coli to the different drugs and the detection rate of drug resistance genes increased over time. The mobile colistin resistance (mcr-1) gene was detected in 24.40% of the strains, and these strains often carried other drug resistance genes, such as those conferring aminoglycoside, β-lactamase, tetracycline, and sulfonamide resistance. Antimicrobial resistance and drug resistance genes in E. coli were least common in the early fattening stage. The individual detection rates of sul1, sul3, aacC4, aphA3, and mcr-1 were significantly lower (P < 0.05) for the early fattening stage than for the middle and late stages. The rational use of antibiotics, in conjunction with the improvement of the breeding environment during the entire broiler fattening cycle, will be helpful in the development of the poultry industry and the protection of public health.

High prevalence of mcr-1-encoded colistin resistance in commensal Escherichia coli from broiler chicken in Bangladesh

Colistin is a last-resort antimicrobial used for the treatment of human infections caused by multidrug-resistant Gram-negative bacteria. However, colistin is still widely used in intensive poultry production in Bangladesh. We aimed to investigate the dynamics and genetic diversity of colistin-resistant commensal Escherichia coli from broiler chickens. A total of 1200 E. coli strains were characterized from 20 broiler farms at three-time points along the production period. All strains were screened for mcr-1 to mcr-5 genes by a multiplex PCR, and their genetic diversity was measured by repetitive extragenic palindromic (REP)-PCR fingerprinting. Genomic diversity and characterization were performed by whole genome sequencing (WGS). Twenty-five percent of the commensal E. coli strains harbored mcr-1 genes. Frequency of mcr-1 gene detection correlated positively (odds ratio 1.71; 95% CI 0.96-3.06; p = 0.068) with the use of colistin in poultry flocks. REP-PCR profiles and WGS analysis showed diverse E. coli population carrying multiple antimicrobial resistance genes. Phylogenetic comparison of mcr-1-bearing strains recovered from this study with a global strain collection revealed wide phylogenetic relationship. This study identified a high prevalence of mcr-1 gene among genetically diverse E. coli populations from broiler chickens in Bangladesh suggesting a massive horizontal spread of mcr-1 rather than by clonal expansion.

A complex approach to a complex problem: the use of whole-genome sequencing in monitoring avian-pathogenic Escherichia coli – a review

Infections associated with Escherichia coli are responsible for immense losses in poultry production; moreover, poultry products may serve as a source of pathogenic and/or resistant strains for humans. As early as during the first hours of life, commercially hatched chickens are colonized with potentially pathogenic E. coli from the environment of hatcheries. The source of contamination has not been quite elucidated and the possibility of vertical spread of several avian pathogenic E. coli (APEC) lineages has been suggested, making the hatcheries an important node where cross-contamination of chicken of different origin can take place. The recent technological progress makes the method of whole-genome sequencing (WGS) widely accessible, allowing high-throughput analysis of a large amount of isolates. Whole-genome sequencing offers an opportunity to trace APEC and extended-spectrum/plasmid-encoded AmpC beta-lactamases-producing E. coli (ESBL/pAmpC-E.coli) along the poultry processing chain and to recognize the potential pathways of “epidemicˮ sequence types. Data from WGS may be used in monitoring antimicrobial resistance, comparative pathogenomic studies describing new virulence traits and their role in pathogenesis and, above all, epidemiologic monitoring of clonal outbreaks and description of different transmission routes and their significance. This review attempts to outline the complexity of poultry-associated E. coli issues and the possibility to employ WGS in elucidating them.

Management factors influencing the occurrence of cellulitis in broiler chickens

One of the main reasons for condemning fattening broiler chickens during meat inspection is cellulitis, which demonstrates the great economic issue concerning this topic. The aim of this epidemiological study was therefore to identify risk factors in order to draw conclusions on how to prevent the occurrence of cellulitis in broilers by implementing management changes. The data were collected between April and November 2018 on conventional broiler farms (n = 100) in the north of Germany with one to fourteen poultry houses per farm. In total, data were collected from 199 broiler flocks with a total of 5,332,767 broilers. Data on the type of management (feeding- and drinking management, housing, lighting management, litter type and animal health) were collected via a questionnaire, with additional data on condemnation rates being provided by the abattoirs. It was found that litter additives like fennel, eucalyptus and probiotics as well as a moist litter quality were associated with lower cellulitis condemnation rates. Flocks fattened in windowless barns, but with relatively higher lux-values as well as those broilers examined in a lower number of housing inspections had significantly lower cellulitis condemnation rates compared to other husbandry systems. In addition, lower cellulitis rates were seen when housing capacities were smaller, regardless of stocking density. The source of the breeders and hatchery also had a significant influence on the occurrence of cellulitis. No correlation was found between the condemnation rates due to cellulitis and the performance of thinning, the water source used, the use of drinking additives, observational skills and number of herd managers monitoring the broilers, participation in an animal welfare programme, the technique of heating and ventilation systems used, the feed supplier, litter material, the broiler breed, the length of darkness periods and chick losses during the first seven days. We concluded that management decisions that lead to stress reduction in the broiler flocks are beneficial in terms of chicken welfare and occurrence of cellulitis.

Whole genome sequence comparison of avian pathogenic Escherichia coli from acute and chronic salpingitis of egg laying hens

BACKGROUND

Infection in the oviduct (salpingitis) is the most common bacterial infection in egg laying hens and is mainly caused by Escherichia coli. The disease is responsible for decreased animal welfare, considerable economic loss as well as a risk of horizontal and vertical transmission of pathogenic E. coli. The outcome of salpingitis may be either acute or chronic. It has not yet been clarified whether the pathological manifestation is a result of the characteristics of the E. coli or whether the manifestation is associated with host factors such as host immunity.

RESULTS

From the core- and accessory genome analysis and comparison of 62 E. coli no genetic markers were found to be associated to either acute or chronic infection. Twenty of the 62 genomes harboured at least one antimicrobial resistance gene with resistance against sulfonamides being the most common. The increased serum survival and iron chelating genes iss and iroN were highly prevalent in genomes from both acute and chronic salpingitis.

CONCLUSION

Our analysis revealed that no genetic markers could differentiate the E. coli isolated from acute versus chronic salpingitis in egg laying hens. The difference in pathological outcome may be related to other factors such as immunological status, genetics and health of the host. These data indicate that salpingitis is another manifestation of colibacillosis.

Comparison and assessment of necropsy lesions in end-of-lay laying hens from different housing systems in Denmark

Apperantly healthy laying hens at the end of production (60 to 91 wk) were investigated for the occurrence of pathology and bacterial infections. In total, 7,477 hens from 15 flocks representing the following production systems: Enriched cages, barn housed layers, and organic/free range layers were necropsied. Indications of bacterial infection were investigated by bacteriological cultivation. The overall prevalence of lesions was 16.60%, including lesions of both infectious and non-infectious origin. The most prevalent lesions were bursitis presternalis (6.65%), reproductive tract lesions (e.g., salpingitis and/or peritonitis and/or oophoritis) (3.50%), serosal scarification (e.g., fibrotic adhesive peritonitis) 1.55%, and neoplasm 1.73%. Significant differences were observed between different production systems and/or flocks in the prevalence of reproductive tract lesions, bursitis presternalis, serosal scarification, skin infections, juvenile hens, and traumas/fractures. No significant difference was observed between different production systems in the prevalence of neoplasia, infection of septicemic etiology, and pododermatitis. In total, 3.4% of the hens were out of lay, with significantly higher rate in organic flocks. Infections of the reproductive tract were the most prevalent lesions with bacterial etiology in all productions systems. In total, 40% of the hens with lesions associated to the oviduct were out of lay and significant difference between production systems were observed. Escherichia coli was the most commonly isolated bacteria and in 90% of the cases they were isolated from the reproductive tract lesions. The second most prevalent bacteria was Gallibacteruim anatis. Significant difference in the prevalence of E. coli positive hens was observed between production systems (P < 0.05). In conclusion, the prevalence of reproductive tract lesions in apparently healthy end-of-lay laying was higher than indicated in previous reports. These findings support the previous suggestions that E. coli and G. anatis are the major pathogens causing reproductive tract lesions.

Infectious potential of human derived uropathogenic Escherichia coli UTI89 in the reproductive tract of laying hens

Avian pathogenic E. coli (APEC) and human uropathogenic E. coli (UPEC) harbour common virulence factors in spite of being associated with disease in different hosts. APEC strains have been shown to have zoonotic potential. In contrast, it is not known whether UPEC strains can cause infection in immunologically competent hens. The objective of the current study was to compare the ability of the well-characterized UPEC strain, UTI89, and the APEC strain, F149H1S2, to infect human and avian cells in culture and to cause salpingitis in an infection model in adult laying hens. In vitro characterization showed that the strains grew equally well in human urine, and both were able to infect human intestinal (Int407) and bladder (J82) epithelial cell lines, and they survived in avian macrophages (HD11) to the same extent. Groups of adult birds were inoculated with 10⁸ bacteria directly into the oviduct using a surgical procedure. After an infection period of 48 h, bacterial load in the oviduct was determined by dilution series, and pathology was determined based on gross lesions and histological observations. Similar counts of UPEC UTI89 (ST95) and the APEC strain F149H1S2 (ST117) were obtained from tissues of infected birds, and salpingitis as evaluated by clinical score and histopathology was observed to a similar extent after infection with the two strains. Together, the results showed that UPEC UTI89 and APEC F149H1S2 have a similar potential for causing salpingitis in laying hens in the model used. No infection differences were observed between the UPEC UTI89 wild type and a mutant strain with knock-out of the well-known virulence gene, fimH, (UPEC UTI89ΔfimH), showing that the salpingitis model is not suitable for the detection of all UPEC virulence factors.

Identical Genetic Profiles of Escherichia coli Isolates from the Gut and Systemic Organs of Chickens Indicate Systemic Bacterial Dissemination, Most Likely Due to Intestinal Destruction Caused by Histomonosis

In laying and breeding chickens, pathomorphological signs of histomonosis often coincide with colibacillosis. Thus, we investigated the systemic spread of Escherichia coli in chickens affected with histomonosis and colibacillosis by characterizing their pheno- and genotypic profiles. For this, 29 birds from 11 affected flocks were necropsied and up to three E. coli isolates each from intestine, heart, and liver of the birds were isolated. A total of 251 isolates were characterized by serotyping, phylogenetic grouping, detection of virulence-associated genes (VAGs), and pulsed-field gel electrophoresis (PFGE). All birds showed egg peritonitis, and fibrinous typhlitis was additionally recorded in 18 birds. Presence of Histomonas meleagridis in ceca was confirmed by PCR and histopathology. Escherichia coli serotype O2:K1 was found to be the most prevalent (37.4%), whereas 31.1% of strains were not typeable. The majority of isolates collected from the intestine and extraintestinal organs belonged to phylogroups B2 (54.1%), D (21.5%), or A (19.5%). Isolates from these phylogroups harbored a higher number of VAGs. Macrorestriction analysis showed that 60.6% of total isolates from all organs tested were included in eight PFGE types. Isolation of E. coli with identical genomic profiles from the intestine and extraintestinal organs of the same or different birds in the same flock indicates for systemic dissemination of the bacteria, independent of E. coli genotype. Intestinal destruction due to H. meleagridis can be considered as the most plausible cause of bacterial dissemination, ultimately leading to colibacillosis.

Polymorphism of Type I-F CRISPR/Cas system in Escherichia coli of phylogenetic group B2 and its application in genotyping

E. coli of phylogenetic group B2 is responsible for many extraintestinal infections, posing a great threat to health. The relatively polymorphic nature of CRISPR in phylogenetically related E. coli strains makes them potential markers for bacterial typing and evolutionary studies. In the current work, we investigated the occurrence and diversity of CRISPR/Cas system and explored its potential for genotyping. Type I-F CRISPR/Cas systems were found in 413 of 1190 strains of E. coli and exhibited the clustering within certain CCs and STs. And CRISPR spacer contents correlated well with MLST types. The divergence analysis of CRISPR showed stronger discriminatory power than MLST, and CRISPR polymorphism was instrumental for differentiating highly closely related strains. The timeline of spacer acquisition and deletion provided important information for inferring the evolution model between distinct serotypes. Identical spacer sequences were shared by strains with the same H-antigen type but not strains with the same O-antigen type. The homology between spacers and antibiotic-resistant plasmids demonstrated the role of Type I-F system in limiting the acquisition of antimicrobial resistance. Collectively, our data presents the dynamic nature of Type I-F CRISPR in E. coli of phylogenetic group B2 and provides new insights into the application of CRISPR-based typing in the species.

Correlation between footpad lesions and systemic bacterial infections in broiler breeders

Footpad lesions are an important factor in evaluation of animal welfare in broilers regulated by law; however, no legal requirements have been set for the parent birds. Nevertheless, the present study confirms that foot health in broiler breeders declines significantly with increasing age, thus potentially impairing the animal welfare due to pain and discomfort from footpad dermatitis. Furthermore, this is the first report demonstrating a correlation between the presence of footpad lesions and systemic bacterial infections with Gram-positive cocci in broiler breeder birds.

Diversity and Population Overlap between Avian and Human Escherichia coli Belonging to Sequence Type 95

APEC causes a range of infections in poultry, collectively called colibacillosis, and is the leading cause of mortality and is associated with major economic significance in the poultry industry. A growing number of studies have suggested APEC as an external reservoir of human ExPEC, including UPEC, which is a reservoir. ExPEC belonging to ST95 is considered one of the most important pathogens in both poultry and humans. This study is the first in-depth whole-genome-based comparison of ST95 E. coli which investigates both the core genomes as well as the accessory genomes of avian and human ExPEC. We demonstrated that multiple lineages of ExPEC belonging to ST95 exist, of which the majority may cause infection in humans, while only part of the ST95 cluster seem to be avian pathogenic. These findings further support the idea that urinary tract infections may be a zoonotic infection.

Avian-pathogenic Escherichia coli (APEC) is a subgroup of extraintestinal pathogenic E. coli (ExPEC) presumed to be zoonotic and to represent an external reservoir for extraintestinal infections in humans, including uropathogenic E. coli (UPEC) causing urinary tract infections. Comparative genomics has previously been applied to investigate whether APEC and human ExPEC are distinct entities. Even so, whole-genome-based studies are limited, and large-scale comparisons focused on single sequence types (STs) are not available yet. In this study, comparative genomic analysis was performed on 323 APEC and human ExPEC genomes belonging to sequence type 95 (ST95) to investigate whether APEC and human ExPEC are distinct entities. Our study showed that APEC of ST95 did not constitute a unique ExPEC branch and was genetically diverse. A large genetic overlap between APEC and certain human ExPEC was observed, with APEC located on multiple branches together with closely related human ExPEC, including nearly identical APEC and human ExPEC. These results illustrate that certain ExPEC clones may indeed have the potential to cause infection in both poultry and humans. Previously described ExPEC-associated genes were found to be encoded on ColV plasmids. These virulence-associated plasmids seem to be crucial for ExPEC strains to cause avian colibacillosis and are strongly associated with strains of the mixed APEC/human ExPEC clusters. The phylogenetic analysis revealed two distinct branches consisting of exclusively closely related human ExPEC which did not carry the virulence-associated plasmids, emphasizing a lower avian virulence potential of human ExPEC in relation to an avian host.

IMPORTANCE APEC causes a range of infections in poultry, collectively called colibacillosis, and is the leading cause of mortality and is associated with major economic significance in the poultry industry. A growing number of studies have suggested APEC as an external reservoir of human ExPEC, including UPEC, which is a reservoir. ExPEC belonging to ST95 is considered one of the most important pathogens in both poultry and humans. This study is the first in-depth whole-genome-based comparison of ST95 E. coli which investigates both the core genomes as well as the accessory genomes of avian and human ExPEC. We demonstrated that multiple lineages of ExPEC belonging to ST95 exist, of which the majority may cause infection in humans, while only part of the ST95 cluster seem to be avian pathogenic. These findings further support the idea that urinary tract infections may be a zoonotic infection.

Use of a Chicken Embryo Lethality Assay to Assess the Efficacy of Phage Therapy

To combat infectious diseases induced by antibiotic-resistant bacteria in human and animals, phage therapy has regained attention by the scientific community. Before phages can be widely accepted as therapeutics in the same way as antibiotics, convincing detailed applied experimental evidence must be available. The embryonated chicken egg model has been used to study the virulence of many pathogens. We describe here a procedure to test the efficacy of phage therapy to treat colibacillosis using a chicken embryo lethality assay, this being potentially applied to others bacterial infection.

Characterization of Escherichia coli causing cellulitis in broilers

The aim of the study was to investigate cellulitis caused by Escherichia coli which has been responsible for economic and welfare problems in Danish broiler production between 2014 and 2016. The study included 13 flocks with unusually high condemnation rates due to cellulitis during a period of approximately one year. From six flocks, 126 condemned carcasses were collected at a Danish slaughterhouse. Further 272 broilers dead on their own were collected on nine broiler farms from flocks with increased mortality and cellulitis (2 farms included both birds from the rearing period and broilers subsequently condemned). All broilers were subjected to post mortem investigation including bacteriology and 247 E. coli isolates were obtained in pure culture from typical lesions of cellulitis. Two-hundred-thirty six E. coli isolates were investigated by pulsed field gel electrophoresis for clonality and 21 selected strains representing major clones were subsequently multi locus sequence typed allowing comparison to sequence types (ST) in the databases. One dominating PFGE type (A) was found to cause cellulitis on all 13 flocks (67% of all isolates). The clone belonged to ST117, which is well described as a pathogen in poultry, and was the primary agent responsible for cellulitis. Whole genome sequencing of eight E. coli isolates confirmed the close genetic relationship between isolates from the outbreaks and showed the presence of genes predicted to encode for the autotransporter proteins aatA, pic and upaG, reported to be of importance for adhesion of E. coli to eukaryotic cells.

Effect of Different Disinfectants on Bacterial Aerosol Diversity in Poultry Houses

To better understand the effect of different disinfectants on the types and quantities of microorganisms in a broiler chicken house, five different types of disinfectants, including ozone, available chlorine, quaternary ammonium salt, glutaraldehyde, and mixed disinfectant, were used. The broiler house microbial communities were analyzed by high-throughput sequencing combined with air sampling. The results showed that the concentrations of airborne aerobic bacteria in the empty broiler houses after application of different disinfectants were significantly reduced compared to a house untreated with disinfectant (P < 0.05 or P < 0.01), and the number of inhalable particles of airborne aerobic bacteria sharply decreased after disinfection. Of the five disinfectants, the mixed disinfectant had the best disinfection efficacy on the total microbial communities (P < 0.05). A total of 508,143 high-quality sequences were obtained by high-throughput sequencing, which identified 1995 operational taxonomic units. In total, 42 phyla and 312 genera were identified. The structures of airborne microbial communities in the broiler houses after the different disinfectants were applied differed. In the house treated with the mixed disinfectant, the microbial communities containing opportunistic pathogens, such as Escherichia-Shigella, Bacillus, and Pseudomonas, had the lowest abundance, with a significant decrease compared to the house untreated with disinfectant. The alpha diversity index showed low diversity of the microbial communities in the house treated with mixed disinfectant. In contrast to the other four disinfectants, only a small amount of bacteria was detected in the air sample in the house treated with the mixed disinfectant; specifically, only four phyla were found (Proteobacteria, Bacteroidetes, Actinobacteria, and Firmicutes). The mixed disinfectant produced a positive effect on disinfection for four phyla; however, it didn’t thoroughly eliminate them. At genus level, Bacillus, Arenimonas, and Shinella could not be detected in the house treated with the mixed disinfectant, but were detected in houses treated with other disinfectants. The high-throughput sequencing results revealed that the combination of multiple disinfectants exhibited a good disinfection efficacy and that this technique could disinfect the air of broiler houses. These results will help guide the development of a reasonable program for broiler house disinfection.

Transmission and pathogenicity of Gallibacterium anatis and Escherichia coli in embryonated eggs

In laying hens, Escherichia coli (E. coli) and Gallibacterium anatis (G. anatis) are considered the two major pathogens causing reproductive tract disorders, either as single infections or as co-infections. Vertical transmission has been confirmed for E. coli but remains to be clearly demonstrated for G. anatis. The aim of the present study was to investigate the ability of both G. anatis and E. coli at eggshell transmission using an embryonated egg dipping model, and to investigate the possible interaction between the two organisms in an embryonated egg injection model. Embryonated eggs were dipped into brain heart infusion broth containing 10⁸ CFU/ml either of G. anatis 12656-12 liver, E. coli ST95 or E. coli ST141, respectively. E. coli ST95 and ST141 were re-isolated from the interior egg contents in 60% (12/20) and 85% (17/20) of the eggs, respectively, while G. anatis 12656-12 was only re-isolated from the interior egg contents in 6.7% (3/45) eggs. Eggs were injected with 10-1000 CFU of either G. anatis 12656-12, E. coli ST95 or ST141 into the allantoic cavity. As few as 10 CFU of G. anatis 12656-12 resulted in 100% mortality within 24 h post injection whereas the E. coli injected embryos all died at 48 h post injection. Significant difference in CFU counts were observed for G. anatis when compared G. anatis injection group with either of the two G. anatis - E. coli co-injection groups. Sixteen hours post injection, a significant difference in embryo mortality could be observed when comparing co-injected embryonated eggs (G. anatis and E. coli) and single-injected (G. anatis or E. coli) embryonated eggs. In conclusion, bacterial transmission via the eggshell was demonstrated for both G. anatis and E. coli although at different magnitudes. The embryonated egg injection model revealed that G. anatis in particular was highly pathogenic when exposed directly to the developing embryo.

Staphylococcus agnetis, a potential pathogen in broiler breeders

In this study, four broiler parent flocks have been followed from the onset of the production period (week 20) until slaughter (week 60). Every week, approximately ten dead broiler breeders, randomly selected among birds dead on their own, were collected and subjected to a full post mortem analysis including bacteriological examination. In total 997 breeders were investigated and for the first time Staphylococcus agnetis was isolated in pure culture from cases of endocarditis and septicemia from 16 broiler breeders. In addition, the cloacal flora from newly hatched chickens originating from the same four flocks were characterized and S. agnetis was found in pure culture of several newly hatched chickens (n=12) and only in one case in combination with another species. Clonality of the isolates was examined by pulsed-field-gel-electrophoresis which showed indistinguishable patterns in isolates from both broiler breeders and broilers. Three isolates were whole genome sequenced to obtain knowledge on virulence genes. The isolates harbored a number of genes encoding different fibrinogen binding proteins and toxins which might be important for virulence. The present findings demonstrate that S. agnetis may be associated with mortality in broiler breeders. No disease was associated with the broilers which were found positive for S. agnetis in the cloaca.