Bayesian estimation of diagnostic accuracy of fecal culture and PCR-based tests for the detection of Salmonella enterica in California cull dairy cattle

Abstract

Epidemiological studies of low prevalence disease problems are often hindered by the high cost of diagnostic testing. The objective of this study was to evaluate PCR screening of both individual and pooled fecal samples from culled dairy cows for the invA gene of Salmonella followed by culture to determine if the sensitivity and specificity were comparable to the results from traditional culture methods applied to individual samples. Cows from six different dairies were sampled in all four seasons. A total of 240 individual cow fecal samples, 24 fecal pools and 24 pools of 24-hour tetrathionate enrichment broth were tested. Diagnostic sensitivity of PCR screening followed by culture of PCR positive or indeterminate samples (i.e PCR-CUL method) was lower than that of culture (CUL) when applied to individual fecal samples (94.8%, 99.5%), however the specificity was comparable (99.6% and 97.7% respectively). For pools of five fecal samples and pools of five, 24 h tetrathionate broth samples, the specificity of both tests were comparable (∼98%); however, their sensitivity was only comparable in pooled fecal samples (∼93%) but greater for culture compared to PCR-CUL in pooled broth samples (∼99% versus ∼93%). Compared to culture results from testing of individual fecal samples, testing pooled fecal samples by culture had a relative sensitivity of 74% and relative specificity of 96%, testing pooled fecal samples by PCR-CUL resulted in relative sensitivity of 90% and relative specificity of 96%. Testing of pooled 24-hour enrichment broth by PCR-CUL increased the relative sensitivity and specificity to 100%. PCR testing followed by culture of positive or indeterminate samples is a time saving alternative to traditional methods. In addition, pooling of samples may be a useful method for decreasing cost if study aims can accommodate a moderate loss of relative sensitivity.

Dairy management practices associated with multi-drug resistant fecal commensals and Salmonella in cull cows: a machine learning approach

“…Pereira et al (2019) followed six of the same California dairies for a second year showing an increase in Salmonella shedding prevalence (30.6%; 95% CI ). The increase in the prevalence was speculated to be due to increased rainfall and drier summer season and herd changes that occurred during the latter study (Adaska et al, 2020). The latter study explored how the study herd and cow level features were associated with shedding of antimicrobial resistant Salmonella and although 60% of the isolates were pan-susceptible, the remaining isolates were found to be resistant to different medically important antimicrobial drugs (MIAD) defined as antimicrobial drugs (AMD) that are important for therapeutic use in humans, with 12% of the isolates being multidrug resistance to more than two drug classes.…”

“…The California Animal Health and Food Safety (CAHFS) laboratory conducted all the study sample testing for Salmonella as described by Adaska et al (2020). Briefly, 1 g of feces was inoculated into tetrathionate selective enrichment broth and incubated at 37 ± 2 C. The next morning a cotton swab was used to inoculate the overnight broth onto XLD and XLT-4 plates and these were incubated overnight at 37 ± 2 C. H 2 S positive, Salmonella suspect colonies from each set of plates were subcultured onto individual bi-plates (5% sheep blood agar-MacConkey agar) and incubated overnight at 37 ± 2 C. One colony from each bi-plate was used for biochemical testing which included triple sugar iron, urea, motility indole ornithine, citrate, O-nitrophenyl-beta-D-galactopyranoside, and lysine iron agar slants.…”

High Prevalence and Factors Associated With the Distribution of the Integron intI1 and intI2 Genes in Scottish Cattle Herds

“…We used pooled fecal DNA extracts, since testing every individual pat sample in a herd was beyond the scope of this study. Pooling is recognized as an efficient and cost-effective method when screening cattle herds for pathogens (41,42,82). Where identification of carriage by individual animals or samples is not required in a first screen, pooling can maintain sensitivity at the herd level, dependant on the expected prevalence (42,83).…”

“…We used a pooling methodology (41,42) to determine herd status for intI1, intI2, and intI3. In the current study, for each herd, pools comprising five individual fecal DNA extracts were mixed as 10 µl aliquots of each individual extract, to form a 50 µl pool, on ice.…”

Identification of a Sub-Clinical Salmonella spp. Infection in a Dairy Cow Using a Commercially Available Stool Storage Kit

“…Appropriate sample handling is therefore crucial in order to reach a definitive diagnosis. More recently, PCR has been used to detect genetic material from bacteria in samples; it is thought to be quicker and more sensitive than culture-based techniques and is often used to detect pathogens that are difficult to recover from faeces [21]. In this study, Salmonella spp.…”