Core genome multilocus sequence typing (cgMLST) confirms systemic spread of avian pathogenic Escherichia coli (APEC) in broilers with cellulitis

Broiler cellulitis has emerged as an important cause of economic losses for farmers and slaughter plants from carcass condemnation at processing. Avian pathogenic Escherichia coli (APEC) has been identified as the main causative agent. The aim was to characterize E. coli isolated from cellulitis and organs in broilers at slaughter by whole genome sequencing analysis to study if systemic spread could be confirmed. Isolates were collected postmortem from 101 carcasses condemned due to dermatitis/cellulitis from five commercial farms and six flocks. Forty-six isolates were characterised to determine serotypes, sequence types and virulence-associated genes. Analysis by cgMLST was performed to study the genetic similarity between isolates from the same broiler, among birds from the same flock and between flocks. Escherichia coli was isolated from 90% of birds from subcutaneous samples. In 20 broilers, E. coli was isolated from organs in pure culture or mixed with sparse growth of other bacteria. In eight of these, there were post-mortem findings suggestive of systemic bacterial spread. The majority of the isolates from the same bird and flock belonged to the same serotype and sequence type and were genetically indistinguishable, but differed when compared between flocks. Common APEC virulence genes, i.e. chuA, fyuA, hlyF, iroN, irp2, iss, ompT, sitA, TerC, TraT, were present in > 87% of the isolates. We conclude that evidence of systemic spread of E. coli from cellulitis was present in some birds at time of slaughter but cannot be reliably detected at meat inspection

Anticoccidial Vaccination Is Associated with Improved Intestinal Health in Organic Chickens

Simple Summary In recent years, the number of organic chicken farms has increased. Chickens can be infected by single-cell parasites, coccidia, which cause lesions in the lining of the intestine leading to poor growth and sometimes death (coccidiosis). This infection can also lead to overgrowth in the intestine of a bacterium, Clostridium perfringens, that may cause further damage (necrotic enteritis). Prevention is often achieved by adding substances in the feed that will slow down the development of parasites and bacteria, but this is not allowed in organic farming. The aim of this study was to investigate if vaccination against coccidia can prevent these diseases in organic chickens. Vaccinated chickens developed milder gut lesions, had fewer and less damaging C. perfringens, and had similar or higher body weight compared to unvaccinated chickens six weeks after vaccination. No deaths from coccidiosis or necrotic enteritis occurred among vaccinated chickens while some unvaccinated chickens died from these diseases. We conclude that vaccination against coccidia benefits organic chickens. This study provides knowledge supporting further development of the organic chicken industry. The results are also of relevance to the management of coccidiosis and necrotic enteritis in conventional broilers. Eimeria spp. and Clostridium perfringens (CP) are pathogens associated with coccidiosis and necrotic enteritis (NE) in broiler chickens. In this study we evaluated the effect of anticoccidial vaccination on intestinal health in clinically healthy organic Ross 308 chickens. On each of two farms, one unvaccinated flock (A1 and B1) was compared to one vaccinated flock (A2 and B2) until ten weeks of age (WOA). Faecal oocysts were counted weekly, and species were identified by PCR (ITS-1 gene). Lesion scoring, CP quantification and PCR targeting the CP NetB toxin gene were performed at three, four, and six WOA and chickens were weighed. Necropsies were performed on randomly selected chickens to identify coccidiosis/NE. Oocyst shedding peaked at three WOA in all flocks. Later oocyst shedding (E. tenella/E. maxima) in unvaccinated flocks at 5-7 WOA coincided with coccidiosis/NE. Although results differed somewhat between farms, vaccination was associated with lower intestinal lesion scores, reduced caecal CP counts, lower proportions of netB-positive CP, lower body weight at three-four WOA, and similar or slightly increased body weight at six WOA. In conclusion, the intestinal health of organic broilers can benefit from anticoccidial vaccination when oocyst exposure levels are high

Highly Pathogenic Avian Influenza (HPAI H5Nx, Clade 2.3.4.4.b) in Poultry and Wild Birds in Sweden: Synopsis of the 2020-2021 Season

Simple Summary Highly pathogenic avian influenza is a virus-induced contagious disease that has killed a large number of poultry and wild birds in Europe in the recent decade and is an increasing problem worldwide. In the winter of 2020-2021, Sweden experienced its worst period to date when the disease was diagnosed on 15 commercial poultry farms and over 2.2 million birds died or were euthanised. The disease was also diagnosed in 130 wild birds and nine flocks of hobby, game or zoo birds between 1 October 2020 and 30 September 2021. The aim of this article was to describe the influenza situation in Sweden during this period and to add to the knowledge related to the alarming situation with highly pathogenic influenza in birds. The disease caused animal suffering and death in wild and domestic birds and incurred high costs due to losses and extensive measures to stop spread. The outbreak investigations, where contacts were traced and virus strains were compared, concluded that the virus was brought to poultry farms by wild birds in most cases. More research is needed to obtain knowledge on risk factors, biosecurity, and wild bird presence on poultry farms to prevent future disease outbreaks. Highly pathogenic avian influenza (HPAI, Gs/Gd lineage) was introduced to Europe in 2005 and has since caused numerous outbreaks in birds. The 2020-2021 season was the hitherto most devastating when considering bird numbers and duration in Europe. Surveillance data, virologic results and epidemiologic investigations from the 2020-2021 outbreaks in Sweden were analysed. Subtypes H5N8 and H5N5 were detected on 24 farms with poultry or other captive birds. In wild birds, subtypes H5N8, H5N5, H5N1, H5N4, H5Nx were detected in 130 out of 811 sampled birds. There was a spatiotemporal association between cases in wild birds and poultry. Based on phylogeny and epidemiology, most of the introductions of HPAI to commercial poultry were likely a result of indirect contact with wild birds. A definite route of introduction to poultry could not be established although some biosecurity breaches were observed. No spread between farms was identified but airborne spread between flocks on the same farm was suspected. Our findings exemplify the challenges posed by the continuously changing influenza viruses that seem to adapt to a broader species spectrum. This points to the importance of wild bird surveillance, compliance to biosecurity, and identification of risk factors for introduction on poultry farms

RNA-Seqde novo assembly and differential transcriptome analysis of the nematode Ascaridia galli in relation to in vivo exposure to flubendazole

The nematode Ascaridia galli (order Ascaridida) is an economically important intestinal parasite responsible for increased food consumption, reduced performance and elevated mortality in commercial poultry production. This roundworm is an emerging problem in several European countries on farms with laying hens, as a consequence of the recent European Union (EU) ban on conventional battery cages. As infection is associated with slow development of low levels of acquired protective immunity, parasite control relies on repeated use of dewormers (anthelmintics). Benzimidazoles (BZ) are currently the only anthelmintic registered in the EU for use in controlling A. galli and there is an obvious risk of overuse of one drug class, selecting for resistance. Thus we developed a reference transcriptome of A. galli to investigate the response in gene expression before and after exposure to the BZ drug flubendazole (FLBZ). Transcriptional variations between treated and untreated A. galli showed that transcripts annotated as mitochondrial glutamate dehydrogenase and cytochrome P450 were significantly down-regulated in treated worms, whereas transcripts homologous to heat shock proteins (HSP), catalase, phosphofructokinase, and a multidrug resistance Pglycoprotein (PGP1) were significantly up-regulated in treated worms. Investigation of candidate transcripts responsible for anthelmintic resistance in livestock nematodes led to identification of several tubulins, including six new isoforms of beta-tubulin, and several ligandgated ionotropic receptors and ABC-transporters. We discovered several transcripts associated with drug binding and processing genes, but further characterisation using a larger set of worms exposed to BZs in functional assays is required to determine how these are involved in drug binding and metabolism.Funding Agencies|Formas [FORMAS 2013-665]; SNIC through Uppsala Multidisciplinary Centre for Advanced Computational Science (UPPMAX) [b2014242]</p