Biomedical subjects

Ynte H Schukken

Publications and source records attributed to Ynte H Schukken.

11 recordsLinked to original sources

PubMed2006

Use of molecular epidemiology in veterinary practice.

Molecular epidemiology is a relatively new branch of epidemiology that uses molecular biology methods to study health and disease in populations. This article gives an introduction to molecular epidemiologic terminology and methodology and its usefulness in large animal medicine and veterinary public health. Applications in source tracing and vaccine studies and insights into transmission dynamics, host specificity, and niche adaptation of infectious organisms are presented. Examples are drawn from a variety of diseases, organisms, and host species and range from the global level to the individual-animal level.

Animal Diseases↗

PubMed2006

Adherent and invasive Escherichia coli is associated with granulomatous colitis in boxer dogs.

The mucosa-associated microflora is increasingly considered to play a pivotal role in the pathogenesis of inflammatory bowel disease. This study explored the possibility that an abnormal mucosal flora is involved in the etiopathogenesis of granulomatous colitis of Boxer dogs (GCB). Colonic biopsy samples from affected dogs (n = 13) and controls (n = 38) were examined by fluorescent in situ hybridization (FISH) with a eubacterial 16S rRNA probe. Culture, 16S ribosomal DNA sequencing, and histochemistry were used to guide subsequent FISH. GCB-associated Escherichia coli isolates were evaluated for their ability to invade and persist in cultured epithelial cells and macrophages as well as for serotype, phylogenetic group, genome size, overall genotype, and presence of virulence genes. Intramucosal gram-negative coccobacilli were present in 100% of GCB samples but not controls. Invasive bacteria hybridized with FISH probes to E. coli. Three of four GCB-associated E. coli isolates adhered to, invaded, and replicated within cultured epithelial cells. Invasion triggered a "splash"-type response, was decreased by cytochalasin D, genistein, colchicine, and wortmannin, and paralleled the behavior of the Crohn's disease-associated strain E. coli LF 82. GCB E. coli and LF 82 were diverse in serotype and overall genotype but similar in phylogeny (B2 and D), in virulence gene profiles (fyuA, irp1, irp2, chuA, fepC, ibeA, kpsMII, iss), in having a larger genome size than commensal E. coli, and in the presence of novel multilocus sequence types. We conclude that GCB is associated with selective intramucosal colonization by E. coli. E. coli strains associated with GCB and Crohn's disease have an adherent and invasive phenotype and novel multilocus sequence types and resemble E. coli associated with extraintestinal disease in phylogeny and virulence gene profile.

Animals↗

PubMed2005

Evaluation of farm management practices as risk factors for clinical listeriosis and fecal shedding of Listeria monocytogenes in ruminants.

OBJECTIVE: To assess seasonal variation in prevalence of Listeria monocytogenes on ruminant farms and identify management practices associated with ruminant listeriosis and fecal shedding of L. monocytogenes. STUDY DESIGN: Case-control study. SAMPLE POPULATION: 2056 samples of feces, feed, soil, and water from 24 case farms with listeriosis and 28 control farms without listeriosis. PROCEDURE: Samples were collected and evaluated via bacterial culture for L. monocytogenes. Univariate associations between farm management practices and listeriosis and fecal shedding of L. monocytogenes were assessed. Multivariate models were developed to identify farm management practices associated with listeriosis and fecal shedding of L. monocytogenes. RESULTS: The prevalence of L. monocytogenes on cattle, goat, and sheep farms was seasonal, especially in fecal samples, with peak prevalence in winter. Although the prevalence of L. monocytogenes in feedstuffs from small-ruminant farms also peaked during winter, the bacterium was detected at a constant rate in cattle farm feedstuffs throughout the year. Farm management practices, animal health and hygiene, and feedstuff quality and storage were associated with ruminant listeriosis and fecal shedding of L. monocytogenes. CONCLUSIONS AND CLINICAL RELEVANCE: Results suggest that the prevalence of L. monocytogenes on ruminant farms is seasonal, management practices are associated with ruminant listeriosis and fecal shedding of L. monocytogenes, and the epidemiologic features of listeriosis differ in cattle versus small ruminants. Awareness of risk factors may be used to develop control measures to reduce animal disease and introduction of L. monocytogenes into the human food chain.

Animal Husbandry↗

PubMed2005

Cow-level evaluation of a kinetics ELISA with multiple cutoff values to detect fecal shedding of Mycobacterium avium subspecies paratuberculosis in New York State dairy cows.

In control programs for Mycobacterium avium subsp. paratuberculosis (Map), the infection status of the cows in a herd is often obtained by testing (a sample of) the herd with an ELISA that may lack some sensitivity and specificity but that is fast and inexpensive. In New York State (NYS), an unabsorbed kinetics ELISA (KELA) has been used extensively for Map control. The objective of this study was to determine the relative sensitivity and specificity of the KELA for detection of fecal shedding of Map for the NYS dairy cow population, taking into account possible confounders such as different antigen batches and Map prevalence in a herd. The data for the study consisted of all serum samples from NYS dairy cows with concurrent fecal culture results submitted to the NY Animal Health Diagnostic Laboratory (NYAHDL) between 1991 and 1996 (n=10,562). The data represented cows with different levels of fecal shedding from herds with different within-herd Map prevalence, including herds that were whole herd fecal culture negative on repeated testing. The cutoff values were based on the predictive value for fecal shedding obtained with a multiple logistic regression model that included variables for the three antigen batches and the Map prevalence in the herd. The KELA could not distinguish between non-shedders and low shedders ( 30 TCFU) was modeled. The three cutoff values of 65, 135 and 170 were based on low (<0.2), moderate (<0.80) and high (>0.95) probabilities for moderate to heavy fecal shedding. The sensitivity and specificity values relative to culture were 67% and 95.2%, 31% and 99.7%, and 11% and 99.9% for the three cutoff values, respectively. Cutoff values for the KELA decreased for herds with increasing within-herd Map prevalence. For the best positive predictive value of a KELA for moderate to heavy fecal shedding, the cutoff values should be determined based on the apparent within-herd prevalence in a herd.

Animals↗

PubMed2005

Molecular subtyping and characterization of bovine and human Streptococcus agalactiae isolates.

Streptococcus agalactiae causes severe invasive disease in humans and mastitis in cattle. Temporally matched bovine milk isolates and clinical human invasive isolates (52 each) collected in New York State over 18 months were characterized by molecular subtyping and phenotypic methods to probe the interspecies transmission potential of this species. EcoRI ribotyping differentiated 17 ribotypes, and DNA sequencing of the housekeeping gene sodA and the putative virulence gene hylB differentiated 7 and 17 allelic types, respectively. Human and bovine isolates were not randomly distributed between ribotypes or hylB and sodA clusters. The combined analysis of all subtyping data allowed the differentiation of 39 clonal groups; 26 groups contained only bovine isolates, and 2 groups contained both human and bovine isolates. The EcoRI ribotype diversity among bovine isolates (Simpson's numerical index of discrimination [mean +/- standard deviation], 0.90 +/- 0.05) being significantly higher than that among human isolates (0.42 +/- 0.15) further supports that these isolates represent distinct populations. Eight human isolates, but no bovine isolates, showed an IS1548 transposon insertion in hylB, which encodes a hyaluronidase. Based on data for 43 representative isolates, human isolates, on average, showed lower hyaluronidase activities than bovine isolates. Isolates with the IS1548 insertion in hylB showed no hyaluronidase activity. Human and bovine isolates did not differ in their abilities to invade HeLa human epithelial cells. Our data show that (i) EcoRI ribotyping, combined with hylB and sodA sequencing, provides a discriminatory subtype analysis of S. agalactiae; (ii) most human invasive and bovine S. agalactiae isolates represent distinct subtypes, suggesting limited interspecies transmission; and (iii) hyaluronidase activity is not required for all human infections.

Alleles↗

PubMed2005

Multilocus sequence typing of Streptococcus uberis provides sensitive and epidemiologically relevant subtype information and reveals positive selection in the virulence gene pauA.

Control of the bovine mastitis pathogen Streptococcus uberis requires sensitive and epidemiologically meaningful subtyping methods that can provide insight into this pathogen's epidemiology and evolution. Development of a multilocus sequence typing (MLST) scheme based on six housekeeping and virulence genes allowed differentiation of 40 sequence types among 50 S. uberis isolates from the United States (n = 30) and The Netherlands (n = 20). MLST was more discriminatory than EcoRI or PvuII ribotyping and provided subtype data with better epidemiological relevance, e.g., by discriminating isolates with identical ribotypes obtained from different farms. Phylogenetic analyses of MLST data revealed indications of reticulate evolution between genes, preventing construction of a core phylogeny based on concatenated DNA sequences. However, all individual gene phylogenies clearly identified a distinct pauA-negative subtaxon of S. uberis for which housekeeping alleles closely resembled those of Streptococcus parauberis. While the average GC content for five genes characterized was between 0.38 and 0.40, pauA showed a considerably lower GC content (0.34), suggesting acquisition through horizontal transfer. pauA also showed a higher nonsynonymous/synonymous rate ratio (dN/dS) (1.2) compared to the other genes sequenced (dN/dS < 0.12), indicating positive selection in this virulence gene. In conclusion, our data show that (i) MLST provides for highly discriminatory and epidemiologically relevant subtyping of S. uberis; (ii) S. uberis has a recombinatorial population structure; (iii) phylogenetic analysis of MLST data reveals an S. uberis subtaxon resembling S. parauberis; and (iv) horizontal gene transfer and positive selection contribute to evolution of certain S. uberis genes, such as the virulence gene pauA.

Base Sequence↗

PubMed2004

Forecasting clinical disease in pigs: comparing a naive and a Bayesian approach.

In veterinary practice the clinician often evaluates and predicts herd health status over time according to clinical criteria. In this paper, we modeled three different clinical signs among pigs based on longitudinal clinical observations in 15 pig herds. We compared and discussed the outputs from two different approaches for making clinical forecasts in a herd: a naive approach using a simple time series model with previous disease observations as predictors and a Bayesian state space models approach, in which the time lag variable entered into the random component of the model. We used the Markov chain Monte Carlo technique to calculate posterior distributions of the forecasts. For the herd specific forecasts the results showed that there were only minor differences between the forecasts from the simple time series model and the median forecasts from the Bayesian model. However, the credibility intervals from the Bayesian model were wider than the forecasts from the simple model and, therefore the Bayesian model encompassed the variability in the forecasts better. Compared to the statistical model, the simple time series would be easier to implement in a practical setting. However, the latter lacks the inherent "generality" from the statistical model that allows the user to make statements about the distribution of the herds and to predict disease status based on the "average" correlation among the herds. The applicability of the Bayesian approach within a clinical decision-making framework was discussed, with special emphasis on the use of prior information and clinical forecasting.

Animals↗

PubMed2003

A comparison of antimicrobial susceptibility patterns for Staphylococcus aureus in organic and conventional dairy herds.

Selective pressure from antimicrobial use, mutations, or acquisition of foreign resistance determinants mediate antimicrobial resistance. If antimicrobial use is the major selective pressure encouraging the development of resistance, then reduced use should result in decreased resistance. We compared antimicrobial susceptibility patterns of Staphylococcus aureus isolates obtained from milk samples from 22 organic (nonantibiotic using) dairy herds to isolates from 16 conventional dairy herds. Susceptibility testing was performed by disk diffusion, and zone diameters were recorded in millimeters for 144 isolates from organic farms and 117 isolates from conventional farms and were also classified as susceptible or not-susceptible (intermediate and resistant categories combined). Strength of association between high or low use and proportion susceptible was evaluated by Chi-square analysis and differences in mean zone diameter for isolates from organic farms versus isolates from conventional farms were compared by analysis of variance. Analysis was done for each antimicrobial and deemed significant at p < or = 0.05. Differences in antimicrobial susceptibility were observed between S. aureus isolates from organic and conventional herds for seven of the nine antibiotics studied. Herds that were certified organic had S. aureus isolates that were more susceptible to antimicrobials. Overall, S. aureus isolates from both organic and conventional herds showed good susceptibility to most commonly used bovine mastitis antimicrobials; however, isolates from organic herds were significantly more susceptible. Longitudinal studies of herds undergoing the transition to organic farming would help elucidate the dynamics of antimicrobial resistance and the potential return of antimicrobial susceptibility.

Animal Husbandry↗

PubMed2003

Longitudinal study to investigate variation in results of repeated ELISA and culture of fecal samples for Mycobacterium avium subsp paratuberculosis in commercial dairy herds.

OBJECTIVE: To determine sources and amounts of variation in a kinetics ELISA (KELA) and results of culture of fecal samples for Mycobacterium avium subsp paratuberculosis (MAP) in repeated tests of individual cows. ANIMALS: 112 cows on 6 commercial dairy farms in New York. PROCEDURE: A nonrandom longitudinal study was conducted from January 2001 to March 2002. A KELA was performed monthly, and MAP culture was performed bimonthly. Cow- and herd-level data were collected. The KELA and culture results were analyzed by use of models that corrected for clustering within herds and repeated measures on cows. RESULTS: Cows of second or higher lactation had increased KELA values, compared with values for first-lactation cows. Cows had lowest KELA values during the first 15 days in milk; KELA values increased until 60 days in milk and then stabilized. Moderate and heavy shedders had significantly higher KELA values than culture-negative cows, and KELA values of shedders progressively increased over time. On average, the KELA value was significantly increased 132 days after a cow was first detected to be a moderate shedder and 236 days after a cow was first detected to be a low shedder. CONCLUSIONS AND CLINICAL RELEVANCE: Analysis suggests that KELA results vary on a cow-level on the basis of lactation number and stage of lactation. High KELA values indicate heavy fecal shedding, but the KELA is not useful in identifying low and moderate shedders that can require up to 236 days to have a significant increase in KELA value.

Animals↗

PubMed2003

Evaluation of the California mastitis test to detect an intramammary infection with a major pathogen in early lactation dairy cows.

The purpose of this study was to evaluate the usefulness of the California mastitis test (CMT) to detect an intramammary infection caused by a major mastitis pathogen in early lactation cows. The gold standard used for comparison was bacteriological culture of single milk samples. The sensitivity (82.4%) and specificity (80.6%) of a positive CMT were highest on the 4th day of lactation.

Animals↗

PubMedDate not supplied

Monitoring udder health and milk quality using somatic cell counts.

In this article the use of somatic cell counts for monitoring udder health and milk quality is discussed. Somatic cell count dynamics at quarter, cow, herd and population level are discussed and illustrated with examples. Quarter and cow somatic cell counts directly represent the inflammatory status of the mammary gland. Herd and population somatic cell count are related to the inflammatory process in individual cows but much more reflect the udder health status of the herd and the quality of the raw milk in the herd and the population. Application of monitoring tools in herd health management are illustrated using a case study. Understanding infection dynamics requires precise longitudinal data. Monitoring tools are required to find the areas of risk in the herd. It is inevitable that more complete udder health programs and monitoring systems are to be developed and implemented. These programs are necessarily dynamic and complex. Implementation of complete udder health programs should be accompanied by research efforts to further fine-tune these complete udder health control and monitoring programs.

Animals↗