Husbandry and biosecurity of Ontario small poultry flocks

Leonardo Susta, Nancy Brochu, Michele Guerin, Brandon Lillie, Csaba Varga, Marina Brash

The 2-year prospective study about disease surveillance in Ontario small flocks (collaboration between the AHL, OVC, and OMAFRA under the Ontario Animal Health Network framework) was completed in September 2017. The results about pathogen prevalence and causes of morbidity and mortality have been published recently.1,2 The last component of the study included assessment of the demographic characteristics of the participating flocks, through analysis of the results derived from the husbandry and biosecurity questionnaire.

Completing the questionnaire was a requisite for small flock owners to participate in our study, which allowed them to submit their birds for postmortem analysis and microbiological testing to the AHL for a discounted fee. The questionnaire was composed of 41 questions, divided into 2 main subjects: one regarding the flock from which the submitted birds derived (e.g., housing, husbandry, vaccination), and one about the general premises where birds were kept (e.g., presence of bodies of water).

We received 153 valid questionnaires. Most owners (65%) reported chickens as the only poultry raised, 32% raised chickens and at least one other poultry species (i.e., turkeys, waterfowl, gamefowl), and only 2% raised species other than chickens. Most commonly, chickens were kept for egg production (71%), and the most frequently reported reason for keeping birds (answers not mutually exclusive) was personal consumption (69%), keeping birds as pets (38%), and farm gate sales (18%). The majority of owners (75%) had raised birds on their premises for 1 year or more. Owners reported to have acquired birds from many different sources (answers not mutually exclusive), including hatcheries (39%), friends and neighbors (31%), feed stores (16%), and others (49%), such as online advertisements and private breeders.

Only 30% of owners reported to keep birds in an exclusively inside coop or barn; 70% had some type of free-range housing or outdoor access. Overall, owner’s knowledge of effective biosecurity practices was inconsistent or inadequate. For instance, <50% of owners reported to have dedicated shoes or clothing for the coop/barn, <5% reported to use a foot-bath, and >60% reported to allow visitors in the coop/barn, often without biosecurity precautions. Only 37% of owners who sourced birds from hatcheries indicated that birds received vaccination at hatch, while the rest provided a negative answer or were unsure. Only 1 owner reported that birds received additional vaccination on the premises. Based on 61% of questionnaires, some form of medication (e.g., coccidiostat, deworming, antibiotics) had been applied to the flocks in the past 12 mo.

Our results provide baseline characterization of small poultry flocks throughout Ontario, and indicate that management and husbandry practices in these flocks are varied. There are some critical issues, however, that were commonly identified. First, birds are often acquired from non-reputable sources (e.g., private breeders, hatcheries that are not registered through the Ontario Hatchery and Supply Flock Program), increasing the likelihood that birds might be infected at the time of purchase with debilitating pathogens (i.e., Mycoplasma spp.), some of which with zoonotic potential (i.e., Salmonella spp.). Additionally, small flocks hardly ever receive additional vaccinations on farm, underscoring the importance of obtaining birds that are already vaccinated. Although vaccinating small flocks is logistically difficult for even the most well-intentioned owners, purchase of birds from registered hatcheries or co-ops will provide chicks that are protected at least for Marek’s disease virus, or – if ready to lay pullets are sought – for several respiratory pathogens. Marek’s disease and mixed respiratory infections, case in point, were the main causes of death for the birds submitted in our study.2 Lastly, striving for better biosecurity practices will not only decrease the risk of pathogen spread to other flocks (whether commercial or not), but will also reduce the pathogen challenge and avoid precipitating silent respiratory infections, such as mycoplasmosis, if these are already present in small flocks.   AHL


1. Brochu NM, et al. A two-year prospective study of small poultry flocks in Ontario, Canada, part 1: prevalence  of viral and bacterial pathogens. J Vet Diagn Invest 2019;31:327-335.

2. Brochu NM, et al. A two-year prospective study of small poultry flocks in Ontario, Canada, part 2: causes of morbidity and mortality. J Vet Diagn Invest 2019;31:336-342.

New multiplex rtPCR test for 3 psittacine viruses

Daniel Gibson, Nicole Nemeth, Hugues Beaufrère, Csaba Varga, Davor Ojkic, Anna Marom, Leonardo Susta

Psittacine birds (parrots, macaws, etc.) are commonly kept as pets or in private collections. Over the past 20 years, >1,800 psittacine birds have been submitted to the OVC and AHL for postmortem examination, with numerous birds being diagnosed with infection by 3 DNA viruses: aves polyomavirus 1 (AvPyV-1, budgerigar fledgling disease virus), beak-and-feather disease virus (BFDV), and psittacid herpesvirus 1 (PsHV-1). These are important pathogens that can cause significant morbidity and mortality in multiple species of psittacine birds. Until recently, the AHL did not provide molecular tests to detect these viruses, basing the diagnosis mainly on histopathologic evidence and clinical history. Therefore, we developed a multiplex real-time PCR (rtPCR) assay for detection of these 3 viruses and improve the accuracy of diagnosis.

Primers and probes were designed from publically available nucleotide sequences for each virus. In addition to routine analytical validation of the assay, test agreement with histologic diagnoses was performed on archived formalin-fixed, paraffin-embedded (FFPE) tissues from psittacine birds submitted for postmortem examination at the OVC and AHL. To be included in the positive cohort, birds must have showed histologic evidence of infection (i.e., inclusion bodies in tissues). We also included FFPE tissues from presumed virus-negative birds, which showed no signs of viral infection. Results were compared between original histologic diagnoses and rtPCR using percentage agreements to determine in how many cases the tests agreed.

The assay showed high analytical sensitivity, detecting <6 copies of viral DNA per reaction, and 100% specificity as determined by the lack of cross-reactivity with 59 other veterinary infectious agents. Overall, FFPE tissues from 85 psittacine birds were used for diagnostic validation. The multiplex rtPCR assay confirmed 98% of histopathology-positive cases (i.e., those with presence of inclusions), and also identified many subclinical infections that were not detected by histopathology, including coinfections (Fig. 1). Tests showed high overall diagnostic agreement, as confirmed by kappa statistics of 0.71, 0.39, and 0.80 for AvPyV-1, BFDV, and PsHV-1, respectively. Subclinical infections were associated with significantly higher average Ct values compared to cases with histologic evidence of infection for all 3 viruses (Fig. 2), suggesting that subclinical infection is associated with lower viral loads.

Data on the presumed best tissues for testing were opportunistically collected based on the placement of tissues in the paraffin blocks. The most likely samples to return a positive Ct value in infected birds were cassettes including spleen for AvPyV-1, liver or kidney for PsHV-1, and bursa or thymus for BFDV. However, these recommendations will need to be validated by testing single tissues sampled separately at the time of autopsy.

Overall, this new assay has shown good utility to confirm infection by AvPyV-1, BFDV and PsHV-1 in psittacine birds diagnosed by histopathology, as well as to identify silent or latent infections, and will prove to be an effective tool for screening protocols and confirmation of disease also in clinical samples and live birds.   AHL

BDFV coinfection by histopathology.

Figure 1. Venn diagram showing the numbers of psittacine birds infected with each virus as determined by a multiplex rtPCR (n = 85). Asterisk indicates one bird that was diagnosed with a APV:BDFV coinfection by histopathology.

Figure 2. Average Ct values of samples from birds with and without viral inclusion bodies in psittacine birds diagnosed with viral infection by rtPCR (n = 61). For each virus, different letters indicate significant differences using 2-tailed t-tests.

Figure 2. Average Ct values of samples from birds with and without viral inclusion bodies in psittacine birds diagnosed with viral infection by rtPCR (n = 61). For each virus, different letters indicate significant differences using 2-tailed t-tests.