H.M. Scott

A Network-Based Meta-Population Approach to Model Rift Valley Fever Epidemics

Rift Valley fever virus (RVFV) has been expanding its geographical distribution with important implications for both human and animal health. The emergence of Rift Valley fever (RVF) in the Middle East, and its continuing presence in many areas of Africa, has negatively impacted both medical and veterinary infrastructures and human morbidity, mortality, and economic endpoints. Furthermore, worldwide attention should be directed towards the broader infection dynamics of RVFV, because suitable host, vector and environmental conditions for additional epidemics likely exist on other continents; including Asia, Europe and the Americas. We propose a new compartmentalized model of RVF and the related ordinary differential equations to assess disease spread in both time and space; with the latter driven as a function of contact networks. Humans and livestock hosts and two species of vector mosquitoes are included in the model. The model is based on weighted contact networks, where nodes of the networks represent geographical regions and the weights represent the level of contact between regional pairings for each set of species. The inclusion of human, animal, and vector movements among regions is new to RVF modeling. The movement of the infected individuals is not only treated as a possibility, but also an actuality that can be incorporated into the model. We have tested, calibrated, and evaluated the model using data from the recent 2010 RVF outbreak in South Africa as a case study; mapping the epidemic spread within and among three South African provinces. An extensive set of simulation results shows the potential of the proposed approach for accurately modeling the RVF spreading process in additional regions of the world. The benefits of the proposed model are twofold: not only can the model differentiate the maximum number of infected individuals among different provinces, but also it can reproduce the different starting times of the outbreak in multiple locations. Finally, the exact value of the reproduction number is numerically computed and upper and lower bounds for the reproduction number are analytically derived in the case of homogeneous populations.

Clostridium difficile in retail meat and processing plants in Texas

The incidence and severity of disease associated with toxigenic Clostridium difficile have increased in hospitals in North America from the emergence of newer, more virulent strains. Toxigenic C. difficile has been isolated from food animals and retail meat with potential implications of transfer to human beings. The objective of the present study was to determine the prevalence of C. difficile in pork from sausage manufacturing plants and retail meat in Texas. Twenty-three C. difficile isolates were detected from 243 meat samples (9.5%) from 3 sausage-manufacturing plants and 5 retail meat outlets from 2004 to 2009. Twenty-two isolates were positive for toxins A, B, and binary toxin, and were characterized as toxinotype V, PFGE type-NAP7, or “NAP7-variant.” Susceptibilities to 11 antimicrobial agents in the current study were similar to those reported previously for toxinotype V isolates, although the results suggested somewhat reduced resistance than reported for other meat, animal, or human clinical toxinotype V isolates.

Quantification of the blaCMY-2 in feces from beef feedlot cattle administered three different doses of ceftiofur in a longitudinal controlled field trial.

The objective of this longitudinal controlled trial was to quantitatively compare carriage of a gene encoding for ceftiofur-resistance (bla(CMY-2)), standardized to a reference gene (16SrRNA), among total community DNA extracted from fecal samples collected from cattle treated with three different dose regimens of ceftiofur crystalline-free acid (CCFA) versus those untreated (controls). Sixty-one steers were assigned to three treatment regimens and housed in six pens. In each pen, five steers were treated and five were controls (one of the pens had six controls). CCFA administration was as follows: two-thirds dose treatment (4.4 mg/kg, on day 0), single-dose treatment (6.6 mg/kg, on day 0), and three-dose treatment (6.6 mg/kg, on days 0, 6, and 13). Fecal samples were collected on days 0, 3, 7, 10, 14, 18, 21, and 28. The gene copy numbers/gram of feces for bla(CMY-2) and 16SrRNA were determined in total community DNA samples using quantitative real-time PCR. The relationships between the quantities of standardized bla(CMY-2), nonstandardized bla(CMY-2), and nonstandardized 16SrRNA, and the explanatory variables (treatment, time, and treatment x time) were assessed using repeated measures mixed models. There were significant differences in each of the three models with respect to each explanatory variable. Overall, while steers administered three doses and two-thirds dose of CCFA had significantly higher quantities of nonstandardized bla(CMY-2) than controls, the standardized values were lower. The administration of CCFA in feedlot cattle may provide selection pressure favoring higher levels of bla(CMY-2) carriage, but this may also lead to concurrent reductions in the total bacterial population (as reflected by lowered 16SrRNA) during the treatment period.

Selection of Fecal Enterococci Exhibiting tcrB-Mediated Copper Resistance in Pigs Fed Diets Supplemented with Copper

ABSTRACT Copper, as copper sulfate, is increasingly used as an alternative to in-feed antibiotics for growth promotion in weaned piglets. Acquired copper resistance, conferred by a plasmid-borne, transferable copper resistance (tcrB) gene, has been reported in Enterococcus faecium and E. faecalis. A longitudinal field study was undertaken to determine the relationship between copper supplementation and the prevalence of tcrB-positive enterococci in piglets. The study was done with weaned piglets, housed in 10 pens with 6 piglets per pen, fed diets supplemented with a normal (16.5 ppm; control) or an elevated (125 ppm) level of copper. Fecal samples were randomly collected from three piglets per pen on days 0, 14, 28, and 42 and plated on M-Enterococcus agar, and three enterococcal isolates were obtained from each sample. The overall prevalence of tcrB-positive enterococci was 21.1% (38/180) in piglets fed elevated copper and 2.8% (5/180) in the control. Among the 43 tcrB-positive isolates, 35 were E. faecium and 8 were E. faecalis. The mean MICs of copper for tcrB-negative and tcrB-positive enterococci were 6.2 and 22.2 mM, respectively. The restriction digestion of the genomic DNA of E. faecium or E. faecalis with S1 nuclease yielded a band of ∼194-kbp size to which both tcrB and the erm(B) gene probes hybridized. A conjugation assay demonstrated cotransfer of tcrB and erm(B) genes between E. faecium and E. faecalis strains. The higher prevalence of tcrB-positive enterococci in piglets fed elevated copper compared to that in piglets fed normal copper suggests that supplementation of copper in swine diets selected for resistance.

Temporal distributions of respiratory disease events within cohorts of feedlot cattle and associations with cattle health and performance indices.

Bovine respiratory disease complex (BRDC), the most common cause of post-weaning disease in North American beef cattle, is a multifaceted process involving pathogen, host, environment, and management factors. Although the importance of describing and evaluating the timing of BRDC cases has been recognized, a formal analysis of the temporal patterns of BRDC has not been described in the literature. Our objectives were to classify within-cohort temporal patterns of BRDC cases during the first 100 days at risk, using operational data from commercial feedlots, and then to evaluate associations among temporal patterns and common cohort-level measures of feedlot performance and health, while controlling for common potential confounders. We used retrospective cohort-level and individual animal health data (2000-2008) from 10 U.S. feedlots. We defined cumulative distributions representing the timing of cases within cohorts using the daily percentage of cases relative to the total number of cases within a cohort. Wards hierarchical clustering method was used to group cohorts exhibiting similar cumulative distributions of BRDC cases. Linear mixed models and generalized estimating equations then were used to determine associations between temporal patterns and economically important measures of cattle performance (mean daily weight gain, total days on feed, and carcass measures) and health (mortality risk and retreatment risk) outcomes, while accounting for possible confounding variables (gender, arrival month, arrival year, arrival weight, arrival risk classification, cumulative morbidity, and the feedlot itself). Cluster analysis identified seven different cohort-level temporal patterns of BRDC cases. Our independent variable of interest (temporal pattern) was associated with mean daily weight gain, total days on feed, and carcass weight, and the estimated effects were modified by arrival weight category and risk classification. Temporal patterns also were associated with USDA measures of carcass yield and quality that largely affect carcass price. We also found associations among temporal patterns and health outcomes (cumulative mortality and retreatment risk), and these effects were significantly modified by arrival weight and cumulative morbidity. Our results are the first to demonstrate that there are several temporal patterns of BRDC repeatedly observed among cohorts of feedlot cattle, and that these BRDC patterns may differentially affect cattle health and performance.

Occurrence of the transferable copper resistance gene tcrB among fecal enterococci of U.S. feedlot cattle fed copper-supplemented diets.

Copper, an essential micronutrient, is supplemented in the diet at elevated levels to reduce morbidity and mortality and to promote growth in feedlot cattle. Gut bacteria exposed to copper can acquire resistance, which among enterococci is conferred by a transferable copper resistance gene (tcrB) borne on a plasmid. The present study was undertaken to investigate whether the feeding of copper at levels sufficient to promote growth increases the prevalence of the tcrB gene among the fecal enterococci of feedlot cattle. The study was performed with 261 crossbred yearling heifers housed in 24 pens, with pens assigned randomly to a 2�2 factorial arrangement of treatments consisting of dietary copper and a commercial linseed meal-based energy protein supplement. A total of 22 isolates, each identified as Enterococcus faecium, were positive for tcrB with an overall prevalence of 3.8% (22/576). The prevalence was higher among the cattle fed diets supplemented with copper (6.9%) compared to normal copper levels (0.7%). The tcrB-positive isolates always contained both erm(B) and tet(M) genes. Median copper MICs for tcrB-positive and tcrB-negative enterococci were 22 and 4 mM, respectively. The transferability of the tcrB gene was demonstrated via a filter-mating assay. Multilocus variable number tandem repeat analysis revealed a genetically diverse population of enterococci. The finding of a strong association between the copper resistance gene and other antibiotic (tetracycline and tylosin) resistance determinants is significant because enterococci remain potential pathogens and have the propensity to transfer resistance genes to other bacteria in the gut.

blaCTX-M-32 on an IncN Plasmid in Escherichia coli from Beef Cattle in the United States

CTX-M-type enzymes are the most extensively distributed extended-spectrum β-lactamases (ESBLs) conferring resistance to advanced-generation cephalosporins in Enterobacteriaceae worldwide ([1][1]). While these enzymes have also become the most common ESBLs detected in U.S. human infections ([2][2

Effects of chlortetracycline and copper supplementation on antimicrobial resistance of fecal Escherichia coli from weaned pigs

Feed-grade chlortetracycline (CTC) and copper are both widely utilized in U.S. pig production. Cluster randomized experiment was conducted to evaluate the effects of CTC and copper supplementation in weaned pigs on antimicrobial resistance (AMR) among fecal Escherichia coli. Four treatment groups: control, copper, CTC, or copper plus CTC were randomly allocated to 32 pens with five pigs per pen. Fecal samples were collected weekly from three pigs per pen for six weeks. Two E. coli isolates per fecal sample were tested for phenotypic and genotypic resistance against antibiotics and copper. Data were analyzed with multilevel mixed effects logistic regression, multivariate probit analysis and discrete time survival analysis. CTC-supplementation was significantly (99% [95% CI=98-100%]) associated with increased tetracycline resistance compared to the control group (95% [95% CI=94-97%]). Copper supplementation was associated with decreased resistance to most of the antibiotics tested, including cephalosporins, over the treatment period. Overall, 91% of the E. coli isolates were multidrug resistant (MDR) (resistant to ≥3 antimicrobial classes). tetA and blaCMY-2 genes were positively associated (P<0.05) with MDR categorization, while tetB and pcoD were negatively associated with MDR. tetA and blaCMY-2 were positively associated with each other and in turn, these were negatively associated with both tetB and pcoD genes; which were also positively associated with one another. Copper minimum inhibitory concentration was not affected by copper supplementation or by pcoD gene carriage. CTC supplementation was significantly associated with increased susceptibilities of E. coli to copper (HR=7 [95% CI=2.5-19.5]) during treatment period. In conclusion, E. coli isolates from the nursery pigs exhibited high levels of antibiotic resistance, with diverse multi-resistant phenotypic profiles. The roles of copper supplementation in pig production, and pco-mediated copper resistance among E. coli in particular, need to be further explored since a strong negative association of pco with both tetA and blaCMY-2 points to opportunities for selecting a more innocuous resistance profile.

Vancomycin-Resistant Enterococcus faecium Strains Isolated from Community Wastewater from a Semiclosed Agri-Food System in Texas

ABSTRACT Vancomycin-resistant Enterococcus faecium strains (VRE) were isolated from human wastewater but not swine fecal waste from a semiclosed agri-food system in Texas. Forty-nine VRE isolates possessed vanA, and one possessed vanB. Twenty-one pulsed-field gel electrophoresis types were identified and segregated into three groups. There was evidence of clonal dissemination among geographically separated sites.

A multivariable assessment quantifying effects of cohort-level factors associated with combined mortality and culling risk in cohorts of U.S. commercial feedlot cattle.

Economic losses due to cattle mortality and culling have a substantial impact on the feedlot industry. Since criteria for culling may vary and may affect measures of cumulative mortality within cattle cohorts, it is important to assess both mortality and culling when evaluating cattle losses over time and among feedlots. To date, there are no published multivariable assessments of factors associated with combined mortality and culling risk. Our objective was to evaluate combined mortality and culling losses in feedlot cattle cohorts and quantify effects of commonly measured cohort-level risk factors (weight at feedlot arrival, gender, and month of feedlot arrival) using data routinely collected by commercial feedlots. We used retrospective data representing 8,904,965 animals in 54,416 cohorts from 16 U.S. feedlots from 2000 to 2007. The sum of mortality and culling counts for each cohort (given the number of cattle at risk) was used to generate the outcome of interest, the cumulative incidence of combined mortality and culling. Associations between this outcome variable and cohort-level risk factors were evaluated using a mixed effects multivariable negative binomial regression model with random effects for feedlot, year, month and week of arrival. Mean arrival weight of the cohort, gender, and arrival month and a three-way interaction (and corresponding two-way interactions) among arrival weight, gender and month were significantly (P<0.05) associated with the outcome. Results showed that as the mean arrival weight of the cohort increased, mortality and culling risk decreased, but effects of arrival weight were modified both by the gender of the cohort and the month of feedlot arrival. There was a seasonal pattern in combined mortality and culling risk for light and middle-weight male and female cohorts, with a significantly (P<0.05) higher risk for cattle arriving at the feedlot in spring and summer (March-September) than in cattle arriving during fall, and winter months (November-February). Our results quantified effects of covariate patterns that have been heretofore difficult to fully evaluate in smaller scale studies; in addition, they illustrated the importance of utilizing multivariable approaches when quantifying risk factors in heterogeneous feedlot populations. Estimated effects from our model could be useful for managing financial risks associated with adverse health events based on data that are routinely available.