Bayesian methods for estimating pathogen prevalence within groups of animals from faecal-pat sampling

Pathogens such as Escherichia coli O157:H7 and Campylobacter spp. have been implicated in outbreaks of food poisoning in the UK and elsewhere. Domestic animals and wildlife are important reservoirs for both of these agents, and cross-contamination from faeces is believed to be responsible for many human outbreaks. Appropriate parameterisation of quantitative microbial-risk models requires representative data at all levels of the food chain. Our focus in this paper is on the early stages of the food chain-specifically, sampling issues which arise at the farm level. We estimated animal–pathogen prevalence from faecal-pat samples using a Bayesian method which reflected the uncertainties inherent in the animal-level prevalence estimates. (Note that prevalence here refers to the percentage of animals shedding the bacteria of interest). The method offers more flexibility than traditional, classical approaches: it allows the incorporation of prior belief, and permits the computation of a variety of distributional and numerical summaries, analogues of which often are not available through a classical framework. The Bayesian technique is illustrated with a number of examples reflecting the effects of a diversity of assumptions about the underlying processes. The technique appears to be both robust and flexible, and is useful when defecation rates in infected and uninfected groups are unequal, where population size is uncertain, and also where the microbiological-test sensitivity is imperfect. We also investigated the determination of the sample size necessary for determining animal-level prevalence from pat samples to within a pre-specified degree of accuracy.     

A practical approach to calculate sample size for herd prevalence surveys

When designing a herd-level prevalence study that will use an imperfect diagnostic test, it is necessary to consider the test sensitivity and specificity. A new approach was developed to take into account the imperfections of the test. We present an adapted formula that, when combined with an existing piece of software, allows improved planning. Bovine paratuberculosis is included as an example infection because it originally stimulated the work. Examples are provided of the trade-off between the benefit (low number of herds) and the disadvantage (large number of animals per herd and exclusion of small herds) that are associated with achieving high herd-level sensitivity and specificity. We demonstrate the bias in the estimate of prevalence and the underestimate of the confidence range that would arise if we did not account for test sensitivity and specificity.     

The consequences of risk-based surveillance: Developing output-based standards for surveillance to demonstrate freedom from disease

Risk factors associated with high or low long-term incidence of displaced abomasum (DA) or clinical ketosis were studied in 60 Swedish dairy herds, using multivariable logistic regression modelling. Forty high-incidence herds were included as cases and 20 low-incidence herds as controls. Incidence rates were calculated based on veterinary records of clinical diagnoses. During the 3-year period preceding the herd classification, herds with a high incidence had a disease incidence of DA or clinical ketosis above the 3rd quartile in a national database for disease recordings. Control herds had no cows with DA or clinical ketosis. All herds were visited during the housing period and herdsmen were interviewed about management routines, housing, feeding, milk yield, and herd health. Target groups were heifers in late gestation, dry cows, and cows in early lactation. Univariable logistic regression was used to screen for factors associated with being a high-incidence herd. A multivariable logistic regression model was built using stepwise regression. A higher maximum daily milk yield in multiparous cows and a large herd size (p = 0.054 and p = 0.066, respectively) tended to be associated with being a high-incidence herd. Not cleaning the heifer feeding platform daily increased the odds of having a high-incidence herd twelvefold (p < 0.01). Keeping cows in only one group in the dry period increased the odds of having a high incidence herd eightfold (p = 0.03). Herd size was confounded with housing system. Housing system was therefore added to the final logistic regression model. In conclusion, a large herd size, a high maximum daily milk yield, keeping dry cows in one group, and not cleaning the feeding platform daily appear to be important risk factors for a high incidence of DA or clinical ketosis in Swedish dairy herds. These results confirm the importance of housing, management and feeding in the prevention of metabolic disorders in dairy cows around parturition and in early lactation.     

海南不同地区香蕉假茎象甲对几种杀虫剂的敏感性测定

采用虫体浸渍法,测定了海南澄迈和儋州两地的香蕉假茎象甲成虫对480克/升毒死蜱EC、77.5%敌敌畏EC、40%辛硫磷EC、40%丙溴磷EC、25%丙溴?辛硫磷EC、20%三唑磷EC等6种杀虫剂对的敏感性。结果表明,6种药剂对澄迈和儋州两地区的香蕉假茎象甲的毒力大小顺序相同,毒死蜱＞丙溴?辛硫磷＞丙溴磷＞三唑磷＞敌敌畏＞辛硫磷;儋州地区的香蕉假茎象甲对6种药剂的敏感性均高于澄迈地区。     

Evaluation of alternative strategies to prevent Newcastle disease in Cambodia

Velogenic viscerotropic Newcastle disease (vvNCD), which is endemic in Cambodia, can be prevented in theory by a combination of biosecurity and immunization of broiler flocks. The relative contribution of appropriate biosecurity and effective vaccination was quantified at the farm level, applying realistic projections for capital investment, fixed and variable production costs and losses following infection. Non-protected broiler flocks generate a loss when the probability of vvNCD infection exceeds 0.4. Applying both biosecurity and effective vaccination would sustain profitability up to a probability of exposure of 1.0. The benefit to cost ratios for alternative strategies were evaluated for a range of probabilities of exposure to vvNCD extending from 0.1 to 1.0. The benefit-to-cost ratio for biosecurity exceeded unity at a risk of exposure exceeding 0.1, and 0.2 for vaccination and the combination of vaccination and biosecurity respectively. A sensitivity analysis demonstrated that the efficiency of protection, feed cost, and financial consequences of infection markedly affected the projected benefit-to-cost ratios associated with alternative methods of prevention.     

Use of a simulation model to evaluate sampling strategies for characterization of antimicrobial resistance in non-type-specific Escherichia coli isolated from dairy cows

OBJECTIVE: To evaluate various sampling strategies for potential use in measuring prevalence of antimicrobial susceptibility in cattle. SAMPLE POPULATION: 500 isolates of non-type-specific Escherichia coli (NTSEC) isolated from the feces of 50 cows from 2 dairy farms (25 cows/farm and 10 isolates/cow). PROCEDURES: Diameters of inhibition zones for 12 antimicrobials were analyzed to estimate variation among isolates, cows, and farms and then used to determine sampling distributions for a stochastic simulation model to evaluate 4 sampling strategies. These theoretic sampling strategies used a total of 100 isolates in 4 allocations (1 isolate from 100 cows, 2 isolates from 50 cows, 3 isolates from 33 cows, or 4 isolates from 25 cows). RESULTS: Analysis of variance composition revealed that 74.2% of variation was attributable to isolates, 18.5% to cows, and 7.3% to farms. Analysis of results of simulations suggested that when most of the variance was attributable to differences among isolates within a cow, culturing 1 isolate from each of 100 cows underestimated overall prevalence, compared with results for culturing more isolates per cow from fewer cows. When variance was not primarily attributable to differences among isolates, all 4 sampling strategies yielded similar results. CONCLUSIONS AND CLINICAL RELEVANCE: It is not always possible to predict the hierarchical level at which clustering will have its greatest impact on observed susceptibility distributions. Results suggested that sampling strategies that use testing of 3 or 4 isolates/cow from a representative sample of all animals better characterize herd prevalence of antimicrobial resistance when impacted by clustering.     

Comparison of a 2-step insulin-response test to conventional insulin-sensitivity testing in horses

Equine insulin resistance is important because of its association with laminitis. The insulin-response test is described to diagnose insulin resistance in clinical settings. Practitioners may be reluctant to perform this test because of the time needed for the test and the fear of inducing hypoglycemia. The objective of the study was to compare a 2-step insulin-response test with a complete insulin-response test. A complete insulin-response test was performed on 6 insulin-resistant horses and 6 controls. A 2-step insulin-response test consisting of an intravenous injection of 0.1 IU/kg human insulin and blood glucose determination at 0 and 30 min after injection was performed on the same horses. Times to reach a 50% reduction of glucose baseline were compared between tests and horses. All the horses tolerated both tests well. No significant difference was observed between baseline glucose concentrations of insulin-resistant horses and controls (P = 0.09). Time to reach 50% reduction of glucose baseline for controls was not significantly different with the use of the complete insulin-response test or the 2-step test (P = 0.98). For insulin-resistant horses, the time to reach 50% reduction of glucose baseline with the use of the 2-step test was significantly longer than for controls (P = 0.004). With a cut-off time of 30 min, the 2-step test had the same characteristics as the complete test. The 2-step test provided a safe, rapid, and low-cost method to diagnose insulin resistance in horses in a clinical setting.     

首届兽药职业技能大赛参赛选手活菌计数能力分析

通过对首届兽药职业技能大赛62名参赛选手大肠杆菌活菌计数结果进行分析,了解我国兽用生物制品生产企业活菌计数能力的整体水平。每名参赛选手发放大肠杆菌菌液1支．要求参赛选手在规定时间内进行活菌计数并提交计数结果。40％参赛选手活菌计数检验结果满意（25／62）;60％检验结果不满意（37／62）。此次技能大赛体现出我国兽用生物制品生产企业检验人员的活菌计数水平参差不齐,部分检验人员活菌计数能力有待进一步提高。     

Probability of freedom from disease after the first detection and eradication of PRRS in Sweden: Scenario-tree modelling of the surveillance system

In July 2007, PRRS was detected for the first time in Sweden. A total of eight positive herds were identified and various measures were taken to eradicate the disease, including restrictions and slaughter of infected herds. Subsequently, both active and passive surveillance activities were undertaken. This study describes stochastic scenario-tree modelling of all the various surveillance system components, to estimate the current probability that Sweden is free from PRRS. The model includes all actions taken after the first positive herd was detected. The surveillance system components included in the model were as follows: investigations undertaken in association with the outbreak, a serological study based on samples collected at slaughter, samples collected in the national PRRS surveillance programme and passive clinical surveillance. The probability of freedom was estimated in time steps of 1 month, from July to December 2007. After each time step, the calculated posterior probability of freedom from the previous month, combined with the probability of introduction, was used as a prior probability for the next month.The result from the model showed a 99.8% probability that Sweden was free from PRRS at the end of December 2007. The estimated total sensitivity of the surveillance system varied between 81.2% and 94.3% and was highest during the first months after the outbreak. For sensitivity analysis purposes, the model was also applied using higher risks of introduction. However, this did not make considerable difference to the final estimates.     

Accuracy of two commercial enzyme-linked immunosorbent assays for the detection of antibodies to Salmonella spp. in slaughter pigs from Canada

Large discrepancies are usually found when different ELISAs for the diagnosis of pig salmonellosis are compared. Thus, our main goal was to estimate the diagnostic accuracy through Bayesian approaches of two commercial assays (Svanovir™ “test A” and HerdCheck™ “test B”) for the detection of antibodies to Salmonella spp. in slaughter pigs. Previously, we estimated the agreement between both tests and their relative sensitivity (Se) and specificity (Sp) with respect to bacteriology on caecal content and ileocaecal lymph nodes. Test A, at a cut-off OD% ≥20%, indicated higher prevalence than test B (OD% ≥10%) (14.6% vs. 8.6%). Relative Se with respect to overall bacteriology was low (≈30%) and similar for both tests, but the relative Sp was significantly lower for test A compared to B (88% vs. 95%). Both tests failed to detect some pigs infected with Salmonella serogroups B and C₁, which they were supposed to identify. In general, tests showed only fair-to-moderate agreement when they were compared (kappa: 0.41). In the Bayesian models, Se of test A varied between 63% and 77%, while Se of test B was 73%. Sp of A was always lower than that of test B (89% vs. 95%). The implications derived from the use of these imperfect serological tests will have to be accounted for in large-scale Salmonella-control programs.     

Application of individual increase in inbreeding to estimate realized effective sizes from real pedigrees

The objective of this study was to test the performance of a recently proposed methodology for the estimation of realized effective size (N(e)) based on individual increase in inbreeding (DeltaF(i)) on several real pedigrees: (a) an experimental mice population; (b) a closed pedigree of fighting bulls; (c) the Spanish Purebred (SPB, Andalusian) horse pedigree; (d) the Carthusian strain of SPB pedigree; (e) the Spanish Arab horse pedigree; and (f) the Spanish Anglo-Arab horse pedigree. Several reference subpopulations were defined on the basis of generation length in order to consider only animals in the last generation, to assess the influence of the pedigree content on the estimates of N(e). The estimates of realized N(e) computed from DeltaF(i) (Ne) tended to be higher than those obtained from regression on equivalent generations. The new parameter Ne remained approximately stable when pedigree depth achieved about five equivalent generations. Estimates of take into account the genetic history of the populations, the size of their founder population, and the mating policy or bottlenecks caused by poor use of reproducing individuals. The usefulness of the realized N(e) computed from individual increase in inbreeding in real pedigrees is also discussed.     

Standardisation of a coproantigen reduction test (CRT) protocol for the diagnosis of resistance to triclabendazole in Fasciola hepatica

A sheep trial was performed to standardise a coproantigen reduction test (CRT) protocol for the diagnosis of resistance to triclabendazole (TCBZ) in Fasciola hepatica). The CRT employs the BIO K201 Fasciola coproantigen ELISA (Bio-X Diagnostics, Jemelle, Belgium) to test for the presence of F. hepatica coproantigens in a faecal sample. If it is coproantigen-positive, the CRT protocol recommends that faecal samples are re-tested for coproantigens at 14 days post-treatment (dpt), with negative testing at this point indicating TCBZ success. Initial work aimed to confirm the sensitivity of the BIO K201 ELISA for Fasciola infection and investigate whether coproantigens represent a robust reduction marker of TCBZ efficacy. Thirty-eight, indoor-reared sheep were artificially infected with F. hepatica isolates known to be susceptible (Cullompton) and resistant (Sligo) to TCBZ action, respectively. Treatment was administered at 12 weeks post-infection (wpi), with 2 sheep groups, infected with each isolate, culled at 2 and 4 weeks post-treatment (wpt), respectively. Necropsy was performed to confirm treatment efficacy. Individual faecal samples were collected twice-weekly throughout the trial period. Additional work focused on the effect of temperature on faecal sample collection and storage. Faecal samples collected from sheep positive for F. hepatica infection were sub-sampled and left at room temperature. Individual sub-samples were tested by ELISA on consecutive days and these readings compared to the original test result on the day of collection. In addition, ELISA values were compared between faecal sub-samples prepared on the day of sampling and post storage at -20°C. Also, an immunocytochemical study was performed to determine the tissue site of origin of the coproantigen protein in the fluke. Results showed that the BIO K201 ELISA was sensitive for Fasciola coproantigens, with coproantigens detectable from 5 wpi onwards. The suitability of coproantigens as a diagnostic marker of TCBZ efficacy was supported by the absence and presence of coproantigens in TCBZ-treated Cullompton (TCBZ-susceptible) and Sligo (TCBZ-resistant) F. hepatica infections at 2 and 4 wpt, respectively. Study results suggest that low to moderate temperature has little, if any, impact on coproantigen stability in faecal samples, but that higher temperatures may have. Immunolabelling for the coproantigen showed that it was specific to the gastrodermal cells of both adult and juvenile flukes.     

Ultrasonographic quantitative evaluation of acute and chronic renal disease using the renal cortical thickness to aorta ratio in dogs

The renal cortical thickness (RCT) has been correlated with renal function. Previous studies have also reported that the RCT:Abdominal aorta(Ao) ratio is constant in normal dogs with various physical factors. This multi-center, retrospective, analytical study aimed to determine if there are differences between actual RCT and predicted value of RCT considering physical factors in dogs with acute or chronic renal disease. We also aimed to demonstrate whether the RCT and Ao ratio index would be useful for evaluating renal pathology. A total of 54 dogs with acute or chronic renal disease and 30 normal healthy dogs were included in this study. The RCT was measured at the center of the renal pyramid as the shortest distance perpendicular to the renal capsule from the base of the renal medullary pyramid at three points. The diameter of the Ao was measured just caudal to the branch of the left renal artery in the sagittal plane in systole. The RCT:Ao ratio of chronic kidney disease (CKD) patients was 0.50 ± 0.11 (mean ± standard deviation). The RCT:Ao ratio in normal dogs was 0.67 ± 0.07. The RCT:Ao ratio in patients with acute kidney injury (AKI) was 0.83 ± 0.05. There was a statistically significant difference between normal dogs and dogs with CKD (P < 0.001) and between normal dogs and dogs with AKI (P < 0.001). In conclusion, findings from the current study supported using the RCT:Ao ratio as a non-invasive quantitative method for characterizing kidney pathology in dogs with acute or chronic renal disease.     

Cost-effectiveness of diagnostic strategies using quantitative real-time PCR and bacterial culture to identify contagious mastitis cases in large dairy herds

Diagnostic strategies to detect contagious mastitis caused by Mycoplasma bovis, Staphylococcus aureus, and Streptococcus agalactiae in dairy herds during an outbreak have been minimally studied with regard to cost and diagnostic sensitivity. The objective of this cross-sectional study was to compare the cost-effectiveness of diagnostic strategies for identification of infected cows in two California dairy herds during contagious mastitis outbreaks.     

A model to determine sampling strategies and milk inoculum volume for detection of intramammary Staphylococcus aureus infections in dairy cattle by bacteriological culture

A model was developed to evaluate the effects that methods of obtaining milk samples and culture inoculum volumes had on the sensitivity of microbiological culture to detect Staphylococcus aureus intramammary infections (IMI). An assumption was made that milk from mammary quarters infected with S. aureus only contains bacteria intermittently. A modified sine wave function was used to model this intermittent shedding pattern. Specifications for the components of the shedding cycle used in this function were based on quantitative culture results from 54 experimentally infected S. aureus quarters, sampled daily for a period of 30–49 days. The components of the shedding cycle were length in days, peak number of CFU shed per milliliter of milk, and length of time in the cycle when no shedding occurred. These components were used to estimate the model's predicted distribution of S. aureus CFU ml⁻¹ milk when individual quarter milk samples were cultured for S. aureus. The sensitivity of culture for several sampling methods was then calculated. The model predicted that culture of a single quarter milk sample had a sensitivity ranging from 60 to 87% for detection of S. aureus IMI depending on inoculum volume. Quarter milk samples taken on day 1 and repeated either on day 3 or day 4, and cultured separately using 0.1 ml of milk for culture inoculum, were predicted to have sensitivities of 90–95% and 94–99%, respectively. Other milk-sampling strategies examined included culture of a composite milk sample (equal-volume mixture of milk from four separate mammary quarters ) and pooled milk samples in which samples from different milkings (either quarter or composite samples) were mixed together and then cultured. The range of predicted sensitivities of these other sampling strategies was 30–97%. Factors having the greatest impact on the sensitivity of culture, in order of importance were: the type of milk sample, the volume of milk cultured, and the time interval between repeated milk sample collection strategies.     

贵州省猪源沙门氏菌对β-内酰胺类药耐药性及耐药基因分析

为了解贵州省猪源沙门氏菌对β-内酰胺类抗菌药物耐药性及其耐药基因的流行情况,本试验从贵州省9个地区规模养猪场中分离鉴定130株沙门氏菌,采用微量肉汤稀释法测定其对常用的8种β-内酰胺类抗菌药物的敏感性,并用PCR法对β-内酰胺酶耐药基因进行检测。结果显示,沙门氏菌对常用的β-内酰胺类抗菌药物耐药性十分严重,其中对头孢他啶的耐药率为100%,其次是氨苄西林和阿莫西林,耐药率分别为80.77%和76.15%,耐药率最低的是头孢噻呋和头孢氨苄,均为46.15%。所有菌株均为多重耐药,其中最少为二重,占总数的2.31%,最多为八重,占总数的4.62%,多重耐药主要集中在四至七重,占总数的88.46%。PCR结果显示,SHV耐药基因未检出,TEM、OXA、CTX-M 3种基因检出率分别是85%、75%和46%,细菌的耐药性与相关耐药基因的检出率基本呈正相关。结果表明,猪源沙门氏菌对β-内酰胺类药物具有普遍耐药性,其中头孢他啶尤为严重。TEM、OXA、CTX-M基因是贵州省猪源沙门氏菌主要耐药基因,临床日益严重的耐药现象与耐药基因的普遍存在有很大的关系。     

2011年～2012年我国不同地区猪流感血清学监测

为了解猪流感病毒(SIV)在我国的流行情况,本研究对2011年～2012年从不同省市重点地区屠宰场、规模化猪场和个体养殖户采集猪血清样品13044份,以经典H1N1 (CS)、类禽H1N1 (EA)、甲型H1N1(pdm/09)、H3N2、H5N1、H9N2亚型SIV抗原并采用血凝抑制(HI)方法检测.结果显示,2011年～2012年我国猪血清中类禽H1N1亚型SIV抗体平均阳性率比其他亚型高,分别为42.24％和45.89％,2011年甲型H1N1亚型SIV血清抗体平均滴度(GMT)比其他亚型高,GMT为53.32,2012年经典H1N1 GMT比其他亚型高,GMT为73.2.结果表明2011年～2012年我国猪群中H1N1亚型SIV感染较为普遍.     

黑龙江部分地区野鸟源新城疫病毒HN、P基因的克隆和序列分析

为了解野鸟源新城疫病毒(NDV)基因变异情况,我们对14株2005年～2006年分离自黑龙江三江自然保护区和哈尔滨周边地区健康野鸟体内的NDV的HN和P基因分别进行RT-PCR扩增,并将其克隆至pMD18-T载体进行核苷酸序列测定。结果显示:14株野鸟源NDVHN基因开放性阅读框架(ORF)均为1716bp,编码571个氨基酸;P基因开放阅读框均为1188bp,编码395个氨基酸。13株野鸟源NDVHN和P基因核苷酸同源性分别为96.4%～99.8%和95.8%～100%,分别与参考毒株HN和P基因相比,同源性为82.3%～98.7%和78.5%～99.4%。1株野鸟源NDV与参考毒株Mutkeswar的HN和P基因高度同源。分析表明:这14株NDV病毒与我国普遍流行的基因Ⅶ型和基因Ⅲ型NDV具有很高的同源性,提示野鸟与家禽新城疫的发生在流行病学和生态学上有着非常密切的关系。     

Analysis of Ribosome Genotyping and Antimicrobial Resistance in Enterococcus faecalis Isolated from Pigs and Chickens

This study was to investigate the ribosome genotyping and antimicrobial resistance in Enterococcus faecalis strains isolated from 2 large-scale farms in Shanghai.40 isolates were evaluated for their sensitivity to 12 antimicrobial agents by broth microdilution,and the ribosome genotyping (ribotype) was characterized by the Riboprinter^® Microbial Characterization System.The resistance rates of most antimicrobial drug were relatively high and multidrug resistant strains were detected with more than 80%.4 strains of Enterococcus faecalis isolated from pigs were resistant to vancomycin,including 2 strains of vancomycin highly resistant (MIC>64 mg/L) with the same time highly resistant to gentamicin and streptomycin (MIC>2 048 mg/L).The results showed that multidrug resistance of Enterococcus faecalis was a serious issue,and the resistant phenotypes of the same type of ribotype was not entirely consistent.