Cyclic genotyping strategies. III: A comparison of predictive methods for group genotyping

This paper provides an investigation into some of the key practical issues for minimizing the cost of DNA testing. Previous studies focused on maximizing the utility of genotyping by prioritizing individuals for genotyping. For logistical reasons, individuals may have to be genotyped in groups rather than individually, and the best group to genotype is expected to differ from the same-sized group chosen when individuals are genotyped sequentially. In a calibration step, simulated populations and full knowledge of genotypes were used to discover the best group(s) to genotype. The characteristics of these groups were then targeted in an optimization step, using normally available information for group formation in targeted populations. Contrasts were made among predictive indices for: (i) individuals, with genotyping between each individual; (ii) individuals, with genotyping occurring group-at-a-time; and (iii) groups, using group variables as criteria. The results of this investigation allow the determination of the value of moving from individual to group genotyping, reveal the favourable attributes of individuals for group formation, and lead to methods to form groups for genotyping. The approach used has applications in reducing genotyping costs in both experimental and commercial populations for both quantitative trait loci (QTL) detection and monitoring.     

Peripheral washout phenomenon in an animal tumour model: comparison of dynamic magnetic resonance imaging using a small molecular contrast medium with histology*

The peripheral washout sign was first described in delayed dynamic contrast‐enhanced magnetic resonance imaging (DCE‐MRI) using a small molecular contrast medium in solid lesions of the human breast and liver. It was found to be 100% specific for malignant lesions and could therefore potentially be used as an additional noninvasive diagnostic tool differentiating malignant from benign lesions. The origin of this phenomenon has not yet been explained. The objective of this study was to translate the peripheral washout sign as seen in solid tumours in delayed DCE‐MRI in human onto an animal model for further assessment of DCE‐MRI characteristics and histological analysis. Small molecular contrast medium DCE‐MRI was performed over 42 min in experimental colon carcinoma grown subcutaneously in rats. Qualitative and quantitative analyses for evaluation of presence and characteristics of the peripheral washout sign were accomplished, defining four centripetally distributed tumour zones (central, intermediate, peripheral and marginal). One hundred per cent of the carcinomas demonstrated a peripheral washout sign in DCE‐MRI starting at 20 min after bolus injection. Histomorphological analysis was performed for tissue classification and evaluation of microvasculature. Quantitative analysis revealed different enhancement profiles of the four tumour zones. Histology indicated centripetally asymmetric vascularization and vascular endothelial growth factor VEGF/VEGF receptor 2 expression within the tumour tissue. Thus, peripheral washout sign can be translated to an animal model. However, comparison of small molecular contrast medium DCE‐MRI with histology revealed that histology alone does not explain the occurrence of the peripheral washout.     

Expression of the high mobility group A1 (HMGA1) and A2 (HMGA2) genes in canine lymphoma: analysis of 23 cases and comparison to control cases

Overexpression of high mobility group A (HMGA) genes was described as a prognostic marker in different human malignancies, but its role in canine haematopoietic malignancies was unknown so far. The objective of this study was to analyse HMGA1 and HMGA2 gene expression in lymph nodes of canine lymphoma patients. The expression of HMGA1 and HMGA2 was analysed in lymph node samples of 23 dogs with lymphoma and three control dogs using relative quantitative real‐time RT‐PCR. Relative quantity of HMGA1 was significantly higher in dogs with lymphoma compared with reference samples. HMGA2 expression did not differ between lymphoma and control dogs. With the exception of immunophenotype, comparison of disease parameters did not display any differences in HMGA1 and HMGA2 expression. The present findings indicate a role of HMGA genes in canine lymphoma. This study represents the basis for future veterinary and comparative studies dealing with their diagnostic, prognostic and therapeutic values.     

Prevalence of hepatitis E virus infection among people and swine in mainland China: A systematic review and meta‐analysis

Hepatitis E virus (HEV) infection remains an important public health problem, and it is endemic primarily in developing countries. This study aimed to evaluate the seroprevalence of HEV among the general population, occupational population and swine in mainland China and its risk factors based on a systematic review and meta‐analysis. Systematic search from EMBASE, PubMed, Web of Science, Cochrane Library and several Chinese databases, such as Wanfang (WF) Data, China National Knowledge Infrastructure (CNKI), Chinese Science and Technology Periodical Database (VIP) and SINOMED, was searched from inception up to 25 April 2018. The overall seroprevalence of HEV and its corresponding 95% confidence interval (CI) as well as the correlation coefficients between different groups were estimated using stata 12.0 and r ‐3.4.1 software. Potential sources of heterogeneity were explored using subgroup and sensitivity analyses. Twenty‐eight studies with 57,274 participants (including human and swine) were included. The seroprevalence of anti‐HEV immunoglobulin G (IgG) among the general population, occupational population and swine was 27.3% (95% CI: 22.4–32.2), 47.4% (95% CI: 40.1–54.8) and 66.4% (95% CI: 61.7–71.1), respectively. The overall prevalence of IgM among the general population was 1.8% (95% CI: 0.7–2.9). The odds ratio for the occupational population, as compared to the general population, was 2.63. The highest anti‐HEV IgG prevalence (59%) was observed in East China, whereas the lowest (34.8%) was noted in Northeast and North China. In the occupational population, the highest prevalence (77.0%) was observed among swine vendors. Seven studies included 30,392 participants (humans and swine); the correlation coefficient for the prevalence of anti‐HEV IgG between the professional population and adult pigs was 0.88. Sensitivity analyses showed that the stability of results was not considered significant. This research found that HEV is common in China, and contact with pork or other pig products may be an important mode of HEV transmission.     

The Use of Direct‐Fed Microbials to Reduce Shedding of Escherichia coli O157 in Beef Cattle: A Systematic Review and Meta‐analysis

Human illness due to infections with Escherichia coli O157 is a serious health concern. Infection occurs through direct contact with infected animals or their faeces, through contaminated food or water and/or through person‐to‐person transmission. A reduction in faecal E. coli O157 shedding in cattle might reduce the burden of human infections. We used systematic review and meta‐analysis to assess the efficacy of direct‐fed microbials (DFM), compared with placebo or no treatment, fed during the pre‐harvest stage of production in reducing faecal E. coli O157 shedding in beef cattle during field trials. Four electronic databases, Nebraska Beef Reports and review article reference lists were searched. A total of 16 publications assessing faecal shedding at the end of the trial and/or throughout the trial period were included. The majority of publicly disseminated trials evaluated the prevalence of E. coli O157 faecal shedding; only two evaluated the concentration of organisms in faeces. The prevalence of faecal E. coli O157 shedding in cattle is significantly reduced by DFM treatments (summary effect size for all DFM – OR = 0.46; CI = 0.36–0.60). The DFM combination Lactobacillus acidophilus (NP51) and Propionibacterium freudenreichii (NP24) was more efficacious in reducing the prevalence of faecal E. coli O157 shedding at the time of harvest and throughout the trial period compared with the group of other DFM, although this difference was not statistically significant. Furthermore, we found that the combination [NP51 and NP24] treatment was more efficacious in reducing the prevalence of faecal E. coli O157 shedding at the time of harvest and throughout the trial period when fed at the dose of 10⁹ CFU/animal/day than any lesser amount, although this difference was not statistically significant. Feeding beef cattle DFM during the pre‐harvest stage of production reduces the prevalence of E. coli O157 faecal shedding and might effectively reduce human infections.     

Assessing the Existing Information on the Efficacy of Bovine Vaccination against Escherichia coli O157:H7 – A Systematic Review and Meta‐analysis

The objective of this study was to conduct a systematic review and meta‐analysis to evaluate the existing information on the efficacy of commercial vaccination to reduce the prevalence of Escherichia coli O157:H7 in weaned cattle in beef feedlot finishing systems under commercial conditions. Currently, only two commercial vaccines exist, and thus, only publications reporting the use of vaccines targeting type III secreted proteins and/or siderophore receptor and porin proteins (SRP) were considered relevant. A total of 18 studies reporting 45 comparisons were included in this review. Meta‐analyses were conducted variously on (i) pre‐harvest outcomes, (ii) at‐harvest outcomes and (iii) both pre‐harvest and at‐harvest outcomes combined. Overall, efficacy of vaccination was consistently observed. Efficacy and homogeneity of the results was demonstrated for the two‐dose regimen, allowing us to conclude with confidence that the two‐dose approach is efficacious. For pre‐harvest outcomes and two‐dose regimens, the odds ratios (OR) were 0.53 (95% CI = 0.45–0.62) for the two vaccines combined and 0.49 (95% CI = 0.40–0.60) for vaccine targeting type III secreted proteins. The test for heterogeneity among studies yielded a Q test P = 0.354 for the two vaccines combined and Q test P = 0.269 for the vaccine targeting type III secreted proteins, indicating homogeneity in both cases. For pre‐ and at‐harvest outcomes combined and two‐dose regimens, the odds ratios (OR) were 0.52 (95% CI = 0.44–0.61) for the two vaccines combined and 0.45 (95% CI = 0.34–0.60) for vaccine targeting type III secreted proteins. The test for heterogeneity among studies yielded a Q test P = 0.134 for the two vaccines combined indicating homogeneity and Q test P = 0.089 for the vaccine targeting type III secreted proteins indicating heterogeneity. Based on this meta‐analysis, bovine vaccination appears to be an effective approach to the pre‐harvest control of E. coli O157:H7.