Evaluation of Bayesian Hui-Walter and logistic regression latent class models to estimate diagnostic test characteristics with simulated data

Estimation of the accuracy of diagnostic tests in the absence of a gold standard is an important research subject in epidemiology (Dohoo et al., 2009). One of the most used methods the last few decades is the Bayesian Hui-Walter (HW) latent class model (Hui and Walter, 1980). However, the classic HW models aggregate the observed individual test results to the population level, and as a result, potentially valuable information from the lower level(s) is not fully incorporated. An alternative approach is the Bayesian logistic regression (LR) latent class model that allows inclusion of individual level covariates (McInturff et al., 2004). In this study, we explored both classic HW and individual level LR latent class models using Bayesian methodology within a simulation context where true disease status and true test properties were predefined. Population prevalences and test characteristics that were realistic for paratuberculosis in cattle (Toft et al., 2005) were used for the simulation. Individual animals were generated to be clustered within herds in two regions. Two tests with binary outcomes were simulated with constant test characteristics across the two regions. On top of the prevalence properties and test characteristics, one animal level binary risk factor was added to the data. The main objective was to compare the performance of Bayesian HW and LR approaches in estimating test sensitivity and specificity in simulated datasets with different population characteristics. Results from various settings showed that LR models provided posterior estimates that were closer to the true values. The LR models that incorporated herd level clustering effects provided the most accurate estimates, in terms of being closest to the true values and having smaller estimation intervals. This work illustrates that individual level LR models are in many situations preferable over classic HW models for estimation of test characteristics in the absence of a gold standard

High Production of LukMF' in Staphylococcus aureus Field Strains Is Associated with Clinical Bovine Mastitis

Staphylococcus aureus, a major cause of bovine mastitis, produces a wide range of immune-evasion molecules. The bi-component leukocidin LukMF' is a potent killer of bovine neutrophils in vitro. Since the role of LukMF' in development of bovine mastitis has not been studied in natural infections, we aimed to clarify whether presence of the lukM-lukF' genes and production levels of LukMF' are associated with clinical severity of the disease. Staphylococcus aureus was isolated from mastitis milk samples (38 clinical and 17 subclinical cases) from 33 different farms. The lukM-lukF' genes were present in 96% of the isolates. Remarkably, 22% of the lukM-lukF'-positive S. aureus isolates displayed a 10-fold higher in vitro LukMF' production than the average of the lower-producing ones. These high producing isolates were cultured significantly more frequently from clinical than subclinical mastitis cases. Also, the detection of LukM protein in milk samples was significantly associated with clinical mastitis and high production in vitro. The high producing LukMF' strains all belonged to the same genetic lineage, spa-type t543. Analysis of their global toxin gene regulators revealed a point mutation in the Repressor of toxins (rot) gene which results in a non-functional start codon, preventing translation of rot. This mutation was only identified in high LukMF' producing isolates and not in low LukMF' producing isolates. Since rot suppresses the expression of various toxins including leukocidins, this mutation is a possible explanation for increased LukMF' production. Identification of high LukMF' producing strains is of clinical relevance and can potentially be used as a prognostic marker for severity of mastitis

The prevalence and risk factors of subclinical mastitis in water buffalo (Bubalis bubalis) in Bangladesh

Subclinical mastitis (SCM) in water buffalo is responsible for reduced milk yield and quality. This cross-sectional study was carried out to a) estimate the prevalence of SCM, b) identify risk factors associated with SCM, and c) identify farm-level risk factors associated with bulk milk somatic cell count (BMSCC). The buffalo farms included in this study represented five rearing systems: free-range, semi-free-range, household, semi-intensive, and intensive, providing a total of 3491 functional quarters of 880 lactating buffalo on 248 farms. The California mastitis test score was used to identify SCM. Bulk milk samples (n = 242) were used for farm-level BMSCC. Quarter and buffalo-level risk factors for SCM were measured using questionnaires and observations. The overall SCM prevalence was high at 27.9% at the quarter-level (25th and 75th percentiles: 8.3% and 41.7%) and 51.5% at buffalo-level (25th and 75th percentiles: 33.3% and 66.7%). The geometric mean BMSCC was 217,000 cells/mL of milk (ranging from 36,000-1,213,000 cells/mL), which is low on average, but some farms could improve substantially. The buffalo rearing system, udder location (left versus right), teat shape, udder asymmetry, number of milkers, and having a quarantine facility were associated with buffalo udder health. Our findings suggest that mainly using free-range rearing systems may help decrease the prevalence of SCM primarily by employing buffalo breeding and better farm biosecurity, and udder health control strategies can be designed based on our findings

Colonization of Extramammary Sites with Mastitis-Associated S. aureus Strains in Dairy Goats.

Staphylococcus aureus ( S. aureus), a major mastitis pathogen in dairy goats, is classified as a contagious pathogen. Although previous research has shown that extramammary body sites can be colonized with S. aureus, it is unknown whether these sites are reservoirs for intramammary infections. The aim of this research was to determine whether extramammary sites can be colonized with mastitis-associated S. aureus strains in dairy goats. Milk samples were collected from 207 primiparous goats and from 120 of these goats, extramammary site samples (hock, groin, nares, vulva and udder) were collected from a large commercial dairy goat herd in the Netherlands during four sampling visits. Extramammary site swabs and milk samples were (selectively) cultured and S. aureus isolates were spa genotyped. The prevalence of colonization of the extramammary sites at goat level was 51.7% and the prevalence of S. aureus intramammary infections was 7.2%. The nares were colonized most frequently (45%), while the groin area was colonized the least (2.5%). Six spa genotypes were identified in this herd and there was no significant difference in the distribution of spa genotypes between the milk or the extramammary sites ( p = 0.141). Both in the extramammary sites and in the milk, spa genotypes t544 (82.3% and 53.3%) and t1236 (22.6% and 33.3%) were the dominant genotypes. These results show that in goats, extramammary sites, particularly the nares, are frequently colonized with mastitis-associated S. aureus strains. Extramammary sites may, thus, be a source of S. aureus intramammary infections that are not targeted by the intervention measures aimed at preventing transmission from infected udder glands

Urinary excretion of advanced glycation end products in dogs and cats

The present study was conducted with privately owned dogs and cats to investigate whether a relationship exists between the dietary AGEs and the urinary excretion of AGEs, as indication of possible effective absorption of those compounds in the intestinal tract of pet carnivores. For this purpose, data were collected from both raw fed and dry processed food (DPF) fed to dogs and cats, through spot urine sampling and questionnaires. Raw pet food (RF, low in AGE diets) was fed as a primary food source to 29 dogs and DPF to 28 dogs. Cats were categorized into 3 groups, which were RF (n = 15), DPF (n = 14) and dry and wet processed pet food (DWF, n = 25). Urinary-free carboxymethyllysine (CML), carboxyethyllysine (CEL) and lysinoalanine (LAL) were analysed using ultrahigh-performance liquid chromatography (UHPLC)—mass spectrometry, and were standardized for variable urine concentration by expressing the AGE concentrations as a ratio to urine creatinine (Ucr) concentration (µg/µmol Ucr). Urinary excretion of CML, CEL and LAL in dogs fed with DPF was 2.03, 2.14 and 3 times higher compared to dogs fed with RF (p <.005). Similar to the dogs, a significant difference in CML:Ucr, CEL:Ucr and LAL:Ucr between the three diet groups was observed in cats (p-overall < 0.005, ANOVA), in which the RF fed group excreted less AGEs than the other groups. Linear regression coefficients and SE of CML:Ucr, CEL:Ucr and LAL:Ucr showed that body weight and neuter status were significantly correlated with CML and CEL excretion, but not to LAL excretion. Our results revealed a significant correlation between dietary AGEs and urinary excretion of free CML, CEL and LAL, and also showed that endogenous formation of these AGEs occurs in both dogs and cats under physiological conditions.</p

Association of Staphylococcus aureus genotypes with milk or colonization of extramammary sites in Dutch dairy cattle indicates strain variation in reservoirs for intramammary infections

Staphylococcus aureus (S. aureus) is a major mastitis pathogen with a detrimental impact on udder health in dairy cattle. Although S. aureus is generally classified as a contagious mastitis pathogen, control measures aimed at preventing contagious transmission are not always effective. Previous studies showed that various extramammary sites can be colonized with S. aureus and could be a reservoir for S. aureus intramammary infections (IMI). The aim of this study was to determine the prevalence of S. aureus extramammary site colonization in Dutch dairy cattle and to compare the spa genotypes of S. aureus isolates from IMI to spa genotypes of isolates from extramammary sites. Six herds were visited and from cows with a composite milk somatic cell count ≥200,000 cells/mL quarter milk samples and swabs from various extramammary sites (hock, groin, udder cleft, nares, and feces) were taken. Extramammary site samples were processed by a two-step high salt selective culture and presence of S. aureus was confirmed by femA PCR. S. aureus isolates from milk and extramammary sites were compared by spa typing. The cow level colonization varied from 0% to 73%, and the prevalence of IMI in the sampled cows varied from 0% to 61% between herds. The extramammary site with the highest prevalence of colonization was the hock (23%) and the lowest prevalence of colonization was found for the nares (5%) and feces (5%). Spa typing of S. aureus isolates from either extramammary sites or milk showed that in most herds there were one or two predominant S. aureus spa genotypes present. Different S. aureus spa genotypes could be categorized into three groups based on the distribution between milk or extramammary sites: i) predominantly milk associated, ii) associated with both milk and extramammary sites, and iii) associated with extramammary sites. In conclusion, we showed that the prevalence of extramammary site colonization differed significantly between herds and extramammary sites and that specific S. aureus spa genotypes were associated with milk (IMI) or extramammary site colonization. Extramammary S. aureus reservoirs could be a source for IMI that cannot be eradicated by intervention measures aimed at contagious mastitis pathogens

The prevalence and risk factors of subclinical mastitis in water buffalo (Bubalis bubalis) in Bangladesh.

Subclinical mastitis (SCM) in water buffalo is responsible for reduced milk yield and quality. This cross-sectional study was carried out to a) estimate the prevalence of SCM, b) identify risk factors associated with SCM, and c) identify farm-level risk factors associated with bulk milk somatic cell count (BMSCC). The buffalo farms included in this study represented five rearing systems: free-range, semi-free-range, household, semi-intensive, and intensive, providing a total of 3491 functional quarters of 880 lactating buffalo on 248 farms. The California mastitis test score was used to identify SCM. Bulk milk samples (n = 242) were used for farm-level BMSCC. Quarter and buffalo-level risk factors for SCM were measured using questionnaires and observations. The overall SCM prevalence was high at 27.9% at the quarter-level (25th and 75th percentiles: 8.3% and 41.7%) and 51.5% at buffalo-level (25th and 75th percentiles: 33.3% and 66.7%). The geometric mean BMSCC was 217,000 cells/mL of milk (ranging from 36,000-1,213,000 cells/mL), which is low on average, but some farms could improve substantially. The buffalo rearing system, udder location (left versus right), teat shape, udder asymmetry, number of milkers, and having a quarantine facility were associated with buffalo udder health. Our findings suggest that mainly using free-range rearing systems may help decrease the prevalence of SCM primarily by employing buffalo breeding and better farm biosecurity, and udder health control strategies can be designed based on our findings

Nationwide practice and outcomes of endoscopic biliary drainage in resectable pancreatic head and periampullary cancer

BACKGROUND: Guidelines advise self-expanding metal stents (SEMS) over plastic stents in preoperative endoscopic biliary drainage (EBD) for malignant extrahepatic biliary obstruction. This study aims to assess nationwide practice and outcomes. METHODS: Patients with pancreatic head and periampullary cancer who underwent EBD before pancreatoduodenectomy were included from the Dutch Pancreatic Cancer Audit (2017-2018). Multivariable logistic and linear regression models were performed. RESULTS: In total, 575/1056 patients (62.0%) underwent preoperative EBD: 246 SEMS (42.8%) and 329 plastic stents (57.2%). EBD-related complications were comparable between the groups (44/246 (17.9%) vs. 64/329 (19.5%), p = 0.607), including pancreatitis (22/246 (8.9%) vs. 25/329 (7.6%), p = 0.387). EBD-related cholangitis was reduced after SEMS placement (10/246 (4.1%) vs. 32/329 (9.7%), p = 0.043), which was confirmed in multivariable analysis (OR 0.36 95%CI 0.15-0.87, p = 0.023). Major postoperative complications did not differ (58/246 (23.6%) vs. 90/329 (27.4%), p = 0.316), whereas postoperative pancreatic fistula (24/246 (9.8%) vs. 61/329 (18.5%), p = 0.004; OR 0.50 95%CI 0.27-0.94, p = 0.031) and hospital stay (14.0 days vs. 17.4 days, p = 0.005; B 2.86 95%CI -5.16 to -0.57, p = 0.014) were less after SEMS placement. CONCLUSION: This study found that preoperative EBD frequently involved plastic stents. SEMS seemed associated with lower risks of cholangitis and less postoperative pancreatic fistula, but without an increased pancreatitis risk

Identification of LukPQ, a novel, equid-adapted leukocidin of Staphylococcus aureus.

Bicomponent pore-forming leukocidins are a family of potent toxins secreted by Staphylococcus aureus, which target white blood cells preferentially and consist of an S- and an F-component. The S-component recognizes a receptor on the host cell, enabling high-affinity binding to the cell surface, after which the toxins form a pore that penetrates the cell lipid bilayer. Until now, six different leukocidins have been described, some of which are host and cell specific. Here, we identify and characterise a novel S. aureus leukocidin; LukPQ. LukPQ is encoded on a 45 kb prophage (ΦSaeq1) found in six different clonal lineages, almost exclusively in strains cultured from equids. We show that LukPQ is a potent and specific killer of equine neutrophils and identify equine-CXCRA and CXCR2 as its target receptors. Although the S-component (LukP) is highly similar to the S-component of LukED, the species specificity of LukPQ and LukED differs. By forming non-canonical toxin pairs, we identify that the F-component contributes to the observed host tropism of LukPQ, thereby challenging the current paradigm that leukocidin specificity is driven solely by the S-component