Longitudinal Study on Causes of Mortality in Danish Broiler Breeders

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.

Horizontal transfer of probable chicken-pathogenicity chromosomal islands between Staphylococcus aureus and Staphylococcus agnetis

Staphylococcus agnetis is an emerging pathogen in chickens but has been most commonly isolated from sub-clinical mastitis in bovines. Previous whole-genome analyses for known virulence genes failed to identify determinants for the switch from mild ductal infections in cattle to severe infections in poultry. We now report identification of a family of 15 kbp, 17-19 gene mobile genetic elements (MGEs) specific to chicken osteomyelitis and dermatitis isolates of S. agnetis. These MGEs can be present in multiple copies per genome. The MGE has been vectored on a Staphylococcus phage that separately lysogenized two S. agnetis osteomyelitis strains. The S. agnetis genome from a broiler breeder case of ulcerative dermatitis contains 2 orthologs of this MGE, not associated with a prophage. BLASTn and phylogenetic analyses show that there are closely related intact MGEs found in genomes of S. aureus. The genome from a 1980s isolate from chickens in Ireland contains 3 copies of this MGE. More recent chicken isolates descended from that genome (Poland 2009, Oklahoma 2010, and Arkansas 2018) contain 2 to 4 related copies. Many of the genes of this MGE can be identified in disparate regions of the genomes of other chicken isolates of S. aureus. BLAST searches of the NCBI databases detect no similar MGEs outside of S. aureus and S. agnetis. These MGEs encode no proteins related to those produced by Staphylococcus aureus Pathogenicity Islands, which have been associated with the transition of S. aureus from human to chicken hosts. Other than mobilization functions, most of the genes in these new MGEs annotate as hypothetical proteins. The MGEs we describe appear to represent a new family of Chromosomal Islands (CIs) shared amongst S. agnetis and S. aureus. Further work is needed to understand the role of these CIs/MGEs in pathogenesis. Analysis of horizontal transfer of genetic elements between isolates and species of Staphylococci provides clues to evolution of host-pathogen interactions as well as revealing critical determinants for animal welfare and human diseases.

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.

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.

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.

Assessment of listing and categorisation of animal diseases within the framework of the Animal Health Law (Regulation (EU) No 2016/429): antimicrobial-resistant Enterococcus faecalis in poultry

Enterococcus faecalis (E. faecalis) was identified among the most relevant antimicrobial-resistant (AMR) bacteria in the EU for poultry in a previous scientific opinion. Thus, it has been assessed according to the criteria of the Animal Health Law (AHL), in particular criteria of Article 7 on disease profile and impacts, Article 5 on its eligibility to be listed, Annex IV for its categorisation according to disease prevention and control rules as in Article 9 and Article 8 for listing animal species related to the bacterium. The assessment has been performed following a methodology previously published. The outcome is the median of the probability ranges provided by the experts, which indicates whether each criterion is fulfilled (lower bound ≥ 66%) or not (upper bound ≤ 33%), or whether there is uncertainty about fulfilment. Reasoning points are reported for criteria with uncertain outcome. According to the assessment here performed, it is uncertain whether AMR E. faecalis can be considered eligible to be listed for Union intervention according to Article 5 of the AHL (33-66% probability). According to the criteria in Annex IV, for the purpose of categorisation related to the level of prevention and control as in Article 9 of the AHL, the AHAW Panel concluded that the bacterium does not meet the criteria in Sections 1, 2 and 4 (Categories A, B and D; 0-5%, 5-10% and 1-10% probability of meeting the criteria, respectively) and the AHAW Panel is uncertain whether it meets the criteria in Sections 3 and 5 (Categories C and E, 33-66% and 33-66% probability of meeting the criteria, respectively). The animal species to be listed for AMR E. faecalis according to Article 8 criteria are mostly birds of the orders Galliformes and Anseriformes, but also mammals and reptiles can serve as reservoirs.

Development of an aerogenous Escherichia coli infection model in adult broiler breeders

Escherichia coli constitutes an immense challenge to the poultry industry due to its devastating effect on productivity, mortality, and carcass condemnations. To aid future studies on disease mechanisms and interventions, an aerogenous infection model was established in adult broiler breeders. Hens (n = 120) were randomly allocated into six groups receiving either aerosolised E. coli or vehicle, or intratracheal E. coli or vehicle. Replication of aerosol inoculation was performed on distinct days. Alternating euthanasia time points were predetermined in order to evaluate the progression of the disease. All animals were thoroughly necropsied, and bacteriological samples were collected as well as tissues for histopathology. Birds inoculated with E. coli exhibited clinical signs and developed characteristic gross and histopathological lesions of colibacillosis, including splenic fibrinoid necrosis, folliculitis, polyserositis and impaction of parabronchi with fibrinoheterophilic exudate and necrotic debris, as well as positive in situ localisation of intralesional E. coli by immunohistochemistry. This study presents a successful development of a discriminative colibacillosis model through aerosol inoculation of adult broiler breeders. Gross and histopathological lesions characteristic of colibacillosis were established in two independent experiments.

Differential Modulation of 25-hydroxycholecalciferol on Innate Immunity of Broiler Breeder Hens

Simple Summary

No predominant changes between R- vs. Ad-feed intake on leukocyte defense against pathogens were observed in broiler breeder hens despite some differences in inflammatory and respiratory burst responses. Overall, supplemental 25-OH-D₃ had more pronounced effects on the innate immunity of Ad-hens. In vitro studies confirmed the differential effects of 25-OH-D₃ to rescue immune functions altered by glucose and/or palmitic acid exposure.

Abstract

Past immunological studies in broilers focused on juveniles within the rapid pre-slaughter growth period and may not reflect adult immune responses, particularly in breeders managed with chronic feed restriction (R). The study aimed to assess innate immune cell functions in respect to R vs. ad libitum (Ad) feed intake in breeder hens with and without dietary 25-hydroxycholecalciferol (25-OH-D₃) supplementation. Ad-feed intake consistently suppressed IL-1β secretion, respiratory burst, and cell livability in peripheral heterophils and/or monocytes along the feeding trial from the age of 51 to 68 weeks. Supplemental 25-OH-D₃ repressed IL-1β secretion and respiratory burst of both cells mostly in R-hens, but promoted monocyte phagocytosis, chemotaxis, and bacterial killing activity in Ad-hens in accompany with relieved hyperglycemia, hyperlipidemia, and systemic inflammation. Overnight cultures with leukocytes from R-hens confirmed the differential effects of 25-OH-D₃ to rescue immune functions altered by glucose and/or palmitic acid exposure. Studies with specific inhibitors further manifested the operative mechanisms via glucolipotoxicity in a cell type- and function-dependent manner. The results concluded no predominant changes between R- vs. Ad-feed intake on leukocyte defense against pathogens despite some differential differences, but supplemental 25-OH-D₃ exerts more pronounced effects in Ad-hens.

Analysis of genomes of bacterial isolates from lameness outbreaks in broilers

We investigated lameness outbreaks at 3 commercial broiler farms in Arkansas. We isolated several distinct bacterial species from Bacterial Chondronecrosis with Osteomyelitis (BCO) lesions from these 3 farms. The results show that BCO-lameness pathogens on particular farms can differ significantly. We characterized genomes for isolates of the 2 most prevalent species, Escherichia coli and Staphylococcus aureus. Genomes assembled for E. coli isolates from all 3 farms were quite different between farms, and most similar to genomes from different geographical locations and hosts. The E. coli phylogenomics suggests frequent host shifts for this species. Genomes for S. aureus isolates from one farm were highly related to those from chicken isolates from Europe. Highly related isolates have also been characterized from chickens in the Arkansas area for at least a decade. Phylogenomics suggest that this S. aureus has been restricted to poultry for more than 40 y. Detailed analysis of genomes from 2 neighboring clades of S. aureus human and chicken isolates, identifies the acquisition of a specific pathogenicity island in the transition from human to chicken pathogen and that pathogenesis for this clade in chickens may depend on this mobile element. Investigation of the evolution of this chicken-restricted clade from 1980 in Ireland, Poland in 2008, Oklahoma in 2010 and Arkansas in 2019, reveals the acquisition of additional virulence determinants including pathogenicity islands. Isolate-specific genome characterizations will help further our understanding of the disease mechanisms of BCO-lameness, a significant animal welfare issue.

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.

The association between meat inspection codes, footpad lesions and thinning of broiler flocks in the Danish broiler production

The foundation of the condemnation practices in Post-Mortem Inspection (PMI) of poultry should be based on up-to-date scientific evidence about the cause of infection and hence whether the lesions observed are of food safety, animal health or welfare concerns. This study aimed to investigate the association between meat inspection codes, footpad lesions, and thinning of flocks in Danish broiler production. The data set was based on the delivery of chicken flocks to one of the two larger chicken slaughterhouses in Denmark, representing 71 farms, 174 houses, and 4,068 flocks over three years from January 2016 to December 2018. Post-mortem condemnation data of slaughtered chickens recorded and stored in the Danish Quality Assurance System (KIK) database was used in the study. Five potentially causal models were developed to investigate whether there was an association between dermatitis, arthritis, systemic infection, emaciation, mortality and possible explaining factors` (footpad lesion, age at slaughter, scratches, ascites, systemic infection and thinning of the flock). These five ecological logistic regression models were analyzed with the three levels: farm, house, and flock. Data from a total number of 126,137,002 (N) slaughtered chickens recorded in KIK databases were used for modeling and analyses. The prevalence of condemned carcasses was 1.1 % (n = 1,420,812). Overall, 12 individual reasons for condemnation of carcasses were recorded. The most frequently observed reason for condemnation was skin disease (scratches and dermatitis) with a prevalence of 0.5 %. Prevalence of ascites was 0.2 %, discoloration 0.09 %, emaciation 0.09 %, hepatitis 0.09 % and arthritis 0.07 %. In the first model, dermatitis was shown to be positively associated with age at slaughter with an OR = 1.04 (CI95 %: 1.02-1.05), while arthritis was considered an intervening variable. Moreover, there was a small protective effect of thinning of the flock for first and second delivery. There was a positive association between arthritis and age at the time of slaughter with an OR = 1.13 (CI95 %: 1.12-1.15). Systemic infections were associated with scratches with an OR = 24.5 (CI95 %: 16.6-36.3) and footpad lesions with an OR = 1.007 (CI95 %: 1.006-1.008). Further modelling of emaciation and mortality was not considered because of unbalanced groups in the data probably caused by the fact that some condemnation codes were rare. We observed that the most common causal factors of condemnation in the systemic infection models were scratches and footpad lesion, therefore preventing and controlling such lesions could reduce losses. Specific management and environmental etiological factors of the main infections causing condemnation in Danish broilers should be determined.

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.