Browsing by Subject "Animal diseases"
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Item Open Access A Cross-Sectional Study Comparing Torque Teno Virus Infection and Bushmeat Exposure Among Pneumonia Patients: Sarawak, Malaysia(2017) Berkhouse, Hudson TaylorBackground: Torque Teno Virus (TTV) is ubiquitous, possibly zoonotic, and has potential for clinical and global health research application. The goals of the current study were to determine prevalence of TTV among pneumonia patients in two Malaysian hospitals, compare results from qPCR and conventional PCR detection methods, and to compare TTV infection against self-reported exposure to bushmeat products.
Methods: Medical officers obtained plasma, PBMC, and NP swab samples, along with bushmeat exposure information from 34 pneumonia patients in Sibu and Kapit hospitals. Samples were tested for TTV using qPCR. Results were corroborated using conventional PCR. Cornfield’s and McNemar’s exact methods were used to analyze infection by exposure, and agreement between PCR results respectively. Diagnostic abilities of the qPCR test were analyzed using conventional PCR as the gold standard.
Results: Conventional PCR reported 17.65% TTV prevalence, while qPCR reported 91.18%. Household size (OR=0.00, 95% CI=0.00, 0.96) and gender (OR=infinity, 95% CI=1.39, infinity) had statistically significant impacts on odds of infection. The qPCR method showed 100% sensitivity, but 7.69% specificity.
Conclusions: Results suggest low prevalence of TTV within the study population, and reaffirm findings by other researchers that smaller household size and being female are associated with decreased odds of TTV infection. Though statistically insignificant, indications that exposure to bushmeat in general increases odds of TTV infection should be investigated further. Researchers must be aware of differences in diagnostic capabilities between PCR methods for TTV detection when designing their own diagnostic studies or conducting TTV related literature reviews.
Item Open Access A Cross-Sectional Study of Small Mammals for Tickborne Pathogen Infection in Northern Mongolia(2016) Pulscher, Laura AnnIntroduction: Extensive studies on tickborne pathogens (TBPs) have been conducted in developed nations, relatively less has been done in developing nations leaving a large gap of knowledge. Mongolia, a country built upon nomadic culture and pastoralism is an ideal system to study TBPs as the population is at an increased risk due to increased time spent outside herding livestock. Discoveries of TBPs in Mongolia include Babesia spp., Anaplasma spp., Borrelia spp., Rickettsia spp. and tick-borne encephalitis virus. While research has focused on TBPs in humans and ticks in Mongolia, little research has assessed animal reservoirs, specifically small mammal species, as reservoirs for TBPs. This project aimed to 1) identify the role of small mammal species in the ecology of TBPs in Mongolia, specifically Rickettsia spp., Anaplasma spp., and Borrelia spp. using serological and molecular analysis and 2) identify risk factors associated with the prevalence of TBPs in small mammal populations in Mongolia.
Methods: From June to July 2016, rodents were live-trapped, and whole blood, serum and ear biopsy samples were collected. Sixty-four rodents were trapped in three aimags (provinces) in northern Mongolia. Whole blood samples were tested by PCR to detect the presence of Rickettsia spp., Anaplasma spp., and Borrelia spp.. In addition, ear biopsy samples were tested by PCR to detect the presence of Borrelia spp.. All rodents were serologically tested for antibodies to Anaplasma phagocytophilum and Rickettsia rickettsii. A multivariate model was used to assess risk factors for the presence of tickborne pathogens. Risk factors examined included species and sex of animal, location and presence of ticks.
Results: 56.0%, 39.0% and 0.0% of animals were positive by PCR for Borrelia spp., Rickettsia spp. and Anaplasma spp., respectively. 41.9% and 24.2% of animals were seropositive for A. phagocytophilum and Rickettsia rickettsii, respectively. Risk factors found to be important predictors of Borrelia spp. molecular detection included small mammal capture in Tov aimag (OR, 4.1; 95% CI, 1.00 – 16.80), male small mammals (OR, 3.07; 95% CI, 0.99 – 9.51) and ground squirrel species type (OR, 3.24; 95% CI, 0.90 – 11.70). The risk factor found to be an important predictor of Rickettsia spp. molecular detection was Mongolian gerbil species type (OR, 246.5; 95% CI, 20.77 – 2925.88). Presence of ticks on small mammals (OR, 4.62; 95% CI, 0.92 – 23.24) was an important risk factor for A. phagocytophilum antibody detection. No risk factors were identified as being important predictors of antibody detection of R. Rickettsii.
Conclusion: The results of this study provide considerable evidence of TBPs circulating in small mammal populations in Northern Mongolia. Further information on TBPs in ticks, humans, livestock and wildlife reservoirs will be important to address public health interventions for TBPs in Mongolia in the future.
Item Open Access A One Health Perspective on Disease Dynamics: Human Monkeypox Transmission in Sankuru District, Democratic Republic of Congo(2015) McMullen, Chelsea LeeBackground: Reports from the first monkeypox (MPX) active surveillance program in the Democratic Republic of Congo (DRC) in the 1980s determined that the disease was not of epidemic potential, with R0<1. However, during an active surveillance period from 2005-2007, researchers found a 20-fold increase during the last 30 years. The purpose of this study was to analyze the contact data from 2005-07 and compare characteristics to those of the 1980s, and toassess the change in R0 of MPX. Methods: Contact tracing information and samples from active lesions were collected. Samples were screened by PCR and positive cases were ranked by generation and grouped into chains of transmission according to date of rash onset, contact tracing, and location. R0 was determined using calculations provided in the 1980s study and chain size distribution was compared. Results: Of 1407 suspected cases of MPX investigated in 2005-07, 287 provided contact information with an average of 6.22 (range, 1-20) contacts each. Among the 703 positive cases, 408 distinct chains of transmission were identified. Average chain size was 1.75 cases (range, 1-12), with the longest reaching six generations. The crude secondary attack rate (AR) was 0.092, with an effective R0 of 0.576. Discussion: Contact characteristics and types of contacts differed from those of the 1980s program. This analysis found a higher crude secondary attack rate and effective R0. This could be the result of a higher proportion of unvaccinated contacts, or that the virus is better able to transmit between humans with a more limited amount of contact.
Item Open Access Statistical Inference and Community Detection in Proximity and Spatial Proteomics: Resolving the Organization of the Neuronal Proteome(2021) Bradshaw, Tyler WesleyTechnological advances in protein mass spectrometry (MS), aka proteomics, haveenabled high-throughput quantification of spatially-resolved, subcellular-specific proteomes. Biological insight in these experiments depends upon sound statistical analysis. Despite the myriad of existing proprietary and open-source software solutions for statistical analysis of proteomics data, these tools suffer a drawback inherent in any general solution: a loss of specificity. These tools often fail to be easily adapted to analyze experiment-specific designs. I present a flexible, linear mixed-effects model framework for assessing differential abundance in protein mass spectrometry experiments. Combined with methods to identify communities of proteins in biological networks, I extend this framework to perform inference at the level of protein groups or modules. Using these software tools, I demonstrate how module-level insight in proximity and spatial proteomics generates hypotheses that identify foci of biological function and dysfunction which may underlie the neuropathology of disease.
Item Open Access Surveillance for Swine Respiratory and Diarrheal Pathogens at the Human-Animal Interface in Sarawak, Malaysia(2017) Borkenhagen, Laura KimIntroduction: An estimated 75% of emerging infections in humans are zoonotic, posing a serious risk of future pandemics. The large livestock operations and dense human population of Southeast Asia are considered a hot-spot for the generation of novel viruses. The primary objective of this pilot study is to employ novel molecular laboratory analyses to examine evidence that swine pathogens including porcine circovirus 2, porcine rotaviruses, encephalomyocarditis virus, and porcine reproductive and respiratory syndrome virus, may be aerosolized at the animal-interface and that humans working in these environments may be carrying these viruses in their nasal airways.
Methods: This study took place in Sarawak, Malaysia among 11 pig farms, two slaughter houses, and three animal markets in June and July of 2017. Pig fecal, pig oral secretion, bioaerosol, and worker nasal wash samples were collected and analyzed via qRT-PCR for swine viruses. Workers were also surveyed for the nature of their occupational exposure with animals and their perceptions and use of personal protective equipment. Fisher’s Exact p-values and odds ratios were used to identify predictors of virus positivity.
Results: In all, 55 pig fecal, 49 pig oral or water, 21 bioaerosol, and 78 worker nasal wash samples were collected across 16 sites. Of these, 21 (38.2%) pig fecal, 43 (87.8%) pig oral or water, 3 (14.2%) bioaerosol, and 4 (5.1%) worker nasal wash samples were positive for PCV2 by qPCR. Porcine rotavirus C was detected in one (1.8%) pig fecal sample. No porcine rotavirus A or encephalomyocarditis virus was detected. The SYBR-based qRT-PCR assay used for PRRSv resulted in high levels of non-specific binding, omitting its inclusion in this write up. Statistically significant risk factors for PCV2 positivity among humans included having a household member with contact with pigs, farms with 1000 or more pigs, and a higher frequency of spotting rodents on the site. The personal protective equipment perceived as most effective at preventing cross-species infection and with the highest use were showering out of work and wearing dedicated boots. Among the equipment where use differed significantly from perception of efficacy were safety glasses, flu vaccination, showering out, and disposable boots.
Conclusions: Porcine circovirus has been posited as a zoonotic pathogen but limited studies have presented mixed results. Our data support the possibility of conducting a future prospective occupational study of pig workers for infection (not just nasal carriage) with this pathogen. Our data also shed light on contradictions between perception and use of personal protective equipment, stressing a need for education in farm biosecurity.