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

Abstract

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.

Keywords: APEC; Escherichia coli; Mortality; antimicrobial resistance; avian pathogenic E. coli; colibacillosis; pathology; surveillance; whole-genome sequencing.

Figure 1

Lesions observed at post-mortem examination. A Chronic perihepatitis. The bird had multiple chronic lesions consistent with polyserositis, e.g., opaque and thickened thoracic air sacs, chronic adhesive pericarditis, and numerous adhesions between several parts of the intestines, the mesovarium and salpinx. The ovary of the hen was inactive. B Deposition of urate in the conjunctiva of a hen. Throughout the coelomic cavity and major joints urate deposition was present. The ureters were occluded  by urate and the kidneys were swollen and showed an increased tubular pattern. The ovary was in regression and no egg was present within the oviduct. C Massive cystic enlargement of the oviduct containing fluid with lumps of fibrinopurulent exudate. The ovary was inactive and the remaining coelomic organs were all cranially displaced. D A massive skin laceration with a caudolaterodorsal location consistent with a mating injury. Externally, the wound measured approximately 9 × 5 cm, with multiple internal pockets with presence of necrotic tissue, fibrinopurulent material and bedding. E Fibrinopurulent exudate extending from the wound in D. The hen was not in lay , and the ovary had completely regressed. F A lesion similar to D–E with fibrinopurulent cellulitis extending from the caudodorsal part of the bird to cranial part of the leg. The external measurement of the wound was approximately 5 × 8 cm. The bird was not in lay , and the ovary was in regression with a few atretic follicles present. Fibrinopurulent peritonitis was present. G Purulent peritonitis in a young chicken. The yolk sac appeared grossly normal though a “button” was present in the unhealed umbilicus, and the yolk sac and liver yielded pure growth of E. coli. H Hyperaemia of the yolk sac which contained a partly inspissated content (yolksacculitis). The umbilical area was hyperaemic (omphalitis) extending to the abdominal wall, fibrinous pericarditis and perihepatitis was present as well as fibrinopurulent airsacculitis and peritonitis. I Ulcus ventriculi in a young chicken adjacent to the gastric isthmus.

Figure 2

Phylogenetic tree presenting Escherichia coli obtained during a non-outbreak period. Midpoint rooted phylogenetic tree based on core genome single-nucleotide polymorphisms (SNPs) of the 77 E. coli isolated from Danish broiler breeder and broiler farms. Farm/progeny origin is indicated on the phylogeny, as is colibacillosis status of the host. Colibacillosis defined as presence of fibrinous-, purulent-, fibrinopurulent or mucopurulent exudate inflammation is presented with black circles, whereas the absence is denoted with open circles. §Single-locus variants are observed within the ST10 cluster (ST7321 (n = 3), ST6665 (n = 3) and ST1141 (n = 1)). The tree is based on 222 391 SNPs detected within a ~3.03 Mbp conserved core genome across the collection. *Depicts E. coli isolate E51 used as reference. Scale bar indicates substitutions per site. Among the 77 isolates, 24 were obtained from the liver, 16 from the salpinx, 22 from the lung, and 12 from the yolk sac. The spleen, umbilical area, and a case of arthritis each contributed with a single isolate. Isolates from birds with an absence of lesions consistent with colibacillosis represented isolation sites: liver, lung, salpinx, yolk sac and joint (n = 6, 11, 2, 4 and 1, respectively).