Sampling guidelines for oral fluid-based surveys of group-housed animals

Abstract

Formulas and software for calculating sample size for surveys based on individual animal samples are readily available. However, sample size formulas are not available for oral fluids and other aggregate samples that are increasingly used in production settings. Therefore, the objective of this study was to develop sampling guidelines for oral fluid-based porcine reproductive and respiratory syndrome virus (PRRSV) surveys in commercial swine farms. Oral fluid samples were collected in 9 weekly samplings from all pens in 3 barns on one production site beginning shortly after placement of weaned pigs. Samples (n=972) were tested by real-time reverse-transcription PCR (RT-rtPCR) and the binary results analyzed using a piecewise exponential survival model for interval-censored, time-to-event data with misclassification. Thereafter, simulation studies were used to study the barn-level probability of PRRSV detection as a function of sample size, sample allocation (simple random sampling vs fixed spatial sampling), assay diagnostic sensitivity and specificity, and pen-level prevalence. These studies provided estimates of the probability of detection by sample size and within-barn prevalence. Detection using fixed spatial sampling was as good as, or better than, simple random sampling. Sampling multiple barns on a site increased the probability of detection with the number of barns sampled. These results are relevant to PRRSV control or elimination projects at the herd, regional, or national levels, but the results are also broadly applicable to contagious pathogens of swine for which oral fluid tests of equivalent performance are available.

Assessment of area spread of porcine reproductive and respiratory syndrome (PRRS) virus in three clusters of swine farms

“…As suggested by Rotolo et al. (), our results showed the importance of sampling all barns when determining disease status of one site. Also important was the fact that the PRRSV status of the sick pen was not consistent across sites, as one would expect that in such immunocompromised population of pigs, PRRSV would be more easily detected once present in a site.…”

“…As sow herds reported a PRRS outbreak, veterinarians responsible for all farms within a 3 km radius were contacted and asked to sample all swine sites within the following 60 days of occurrence of the outbreak. This timeframe was chosen based on the suggested time it could take PRRSV to infect the majority of animals within a swine barn (Rotolo et al., ). A radius of 3 km was initially considered for defining participating “clusters” and farms to be sampled, and these clusters were expanded as allowed by allocated resources.…”

“…Oral fluid PCR testing was used to determine PRRSV status of neighbouring farms. The total number of samples per barn was calculated as per recent oral fluid sampling guidelines (Rotolo et al., ). In brief, sample size was calculated using a fixed design prevalence of 50% for a minimum of 99% probability of detection on a site, considering the varying total number of barns for each site and assuming a diagnostic sensitivity and specificity of 95% and 100%, respectively (Rotolo et al., ).…”

“…The total number of samples per barn was calculated as per recent oral fluid sampling guidelines (Rotolo et al., ). In brief, sample size was calculated using a fixed design prevalence of 50% for a minimum of 99% probability of detection on a site, considering the varying total number of barns for each site and assuming a diagnostic sensitivity and specificity of 95% and 100%, respectively (Rotolo et al., ). The relatively high expected prevalence of 50% was used as it would be expected that in order for PRRSV to become airborne, maintain a minimum infectious concentration and reach the pig population in the neighbouring site, the within‐site PRRSV prevalence in a potential source site would need to be considerably high.…”

Gaps in African swine fever: Analysis and priorities

“…Samples obtained through non‐invasive sampling methods such as oral fluid and faeces allow ASFV and anti‐ASFV antibodies detection (Davies et al., ; De Carvalho Ferreira, Weesendorp, Quak, Stegeman, & Loeffen, ; Giménez‐Lirola et al., ; Mur et al., ; Nieto‐Pelegrín, Rivera‐Arroyo, & Sánchez‐Vizcaíno, ). Commercial tests based on oral fluid are already available for porcine reproductive and respiratory syndrome as well as sampling guidelines for oral fluid‐based survey on grouped‐housed animals (Rotolo et al., ). However, standardized methods for sampling and testing ASF on such matrices (oral fluid and faeces) need still to be developed and validated for domestic pig and wild swine populations.…”