382 research outputs found
The risk of STEC (Shiga toxin-producing Escherichia coli) contamination in wild venison
No full textWe have published this report to address knowledge gaps and better understand the risk of STEC (Shiga toxin-producing Escherichia coli) contamination of wild venison.
The report is based on three core objectives to:
- map the venison industry in Scotland
- assess STEC prevalence in wild deer faeces in Scotland
- review cross-contamination risks in the slaughter and processing stages of wild deer from the field to larder
Although the prevalence of STEC O157 in wild deer is low, the report found that when discovered, it is the strain associated with the most severe forms of human disease. Therefore, adherence to strict hygiene practices from cull to final product are strongly recommended within the report.
The venison industry continues to take a cooperative and responsible approach to STEC O157 when found, working to better understand the risks in the sector and how to mitigate them in the interest of public health protection
The microbial condition of Scottish wild deer carcasses collected for human consumption and the hygiene risk factors associated with Escherichia coli and total coliforms contamination
No full textWild deer hunting is necessary in Scotland to control deer population density, with most carcasses being processed for human consumption. As limited information is available on the microbial condition of Scottish venison, we studied the variation of total coliforms and Escherichia coli (E. coli) on 214 wild deer carcasses collected from six approved establishments. Samples were collected from the hide, body cavity and external surface of each carcass and mean values were determined following bacterial plate counts. The mean log10/cm2 coliforms were 5.78 (hide), 6.80 (body cavity) and 6.36 (external surface). The mean log10/cm2 E. coli were 1.82 (hide), 2.27 (body cavity) and 2.17 (external carcass). Significantly higher coliforms counts were associated with storage-to-dressing times above 6 days and with transport distances. Risk factors that increased E. coli were red deer species, ambient temperature above 7°C during hunting, dirty hides, faecal contamination and moisture or slimy film on the carcass. Although the bacterial counts obtained in this study indicated some hygienic processing, for around half of the carcasses, the E. coli counts were above 2 log10/cm2. Therefore, the above risk factors suggest a few handling hygiene practices that should be further improved to enhance quality and safety.<br/
Epidemiology of emerging human-infective RNA viruses: discovery, geographical extent, and disappearance
No full textPrevious investigations into human infectious diseases have revealed RNA
viruses as major etiological agents. Given the recent rate of newly detected
human-infective RNA viruses such as severe acute respiratory syndrome
coronavirus (SARS-CoV), SARS-CoV-2, Middle East respiratory syndrome
coronavirus, and Bundibugyo ebolavirus, targeting virus discovery in high-risk
regions, characterizing viruses with the greatest likelihood of spreading and
establishing sustained infection in humans would benefit better preparedness
for future outbreaks. There is a lack of evidence on determinants of spatio-temporal patterns in the discovery of human-infective RNA viruses, though
previous studies have attempted to identify hotspots of emerging infectious
diseases caused by various pathogens. There are also no quantitative studies
exploring predictors of geographical extent and the disappearance for all
currently known human-infective RNA viruses.
This thesis aimed to address the following gaps.
1. Identifying predictors discriminating between areas with and without
discovery of human-infective RNA viruses and predicting discovery hotspots,
at both global and regional scales. Predictors identified include socio-economic, climatic, land use, and biodiversity variables.
2. Prediction of the geographical extent and the disappearance of human-infective RNA viruses, using features such as taxonomy, virus structure,
transmission mode, host range, origin, and clinical presentation.
3. Taking SARS-CoV-2 as an example, investigating how predictors related to
demographics, socioeconomics, travel, healthcare, co-morbidities, readiness,
geography, COVID-19 testing, and interventions have affected the epidemic
of the disease it caused—coronavirus disease 2019 (COVID-19)—between
countries in the WHO African Region.
In order to address the gaps outlined above, I firstly geocoded the first reports
of 223 human-infective RNA viruses at the global scale. Using a Poisson
boosted regression tree (BRT) model, I identified GDP growth, GDP, and
urbanization as top predictors of virus discovery, and predicted discovery
hotspots including both historical hotspots—eastern North America, Europe,
central Africa, eastern Australia, and north-eastern South America, and new
hotspots—East and Southeast Asia, India, and Central America. Stratified
analyses suggested discovery of vector-borne viruses and strictly zoonotic
viruses was more correlated with climatic variables and biodiversity, whereas
the discovery of non-vector-borne viruses and human-transmissible viruses
was more strongly correlated with GDP and urbanization. Next, I focused on
comparisons of the specific predictors of RNA virus discovery in three different
regions with different GDP—United States, China, and Africa. A similar
methodology as the global analysis was used on each region separately, the
results showed that predictors such as GDP and land use continued to be top
predictors in three regions, but climate and biodiversity variables were
consistently less important predictors than at a global scale.
To identify predictors of the geographical extent and the disappearance (no
record of infection in the literature for the past ten years or more), I collated
information for 223 human-infective RNA viruses on their geographical extents
and persistence in causing human infections from peer-reviewed literature. By
fitting Bernoulli BRT models, I observed that viral features that predicted wide
geographic extent included transmissibility between humans, a +ssRNA
genome, narrow host range [i.e. infecting humans only or humans and other
non-human primates (NHP) only], and having a reservoir host in a NHP.
Viruses were more likely to disappear if they were incapable of transmission
between humans, have had a localised geographic extent, a dsRNA genome,
were non-pathogenic and non-fatal, were firstly discovered through active
discovery programmes rather than passive investigation of the aetiology, and
were transmitted by vectors and direct contact. Results for both geographical
extent and virus disappearance did not change after factoring out reporting
effort. I concluded that multiple characteristics determined the geographical
extent and disappearance of human-infective RNA viruses; however,
transmission mode and structure were consistently the most important
predictors of the geographical extent and disappearance of human-infective
RNA viruses. Host range was an important predictor of geographical extent,
though less important for disappearance. Geographical extent, clinical
presentation and discovery process all contributed to the probability of a virus
disappearing.
To understand the differences between epidemics of COVID-19 between
countries of the WHO African Region, I selected the timing of the first case and
the mortality rate in the first and second waves as the three outcomes. By
applying a series of statistical models including Cox proportional hazards
regression models, generalized linear mixed models and multinomial logistic
regression models, I found that COVID-19 in Africa arrived earlier and caused
greater mortality in countries with more pre-pandemic international
connectivity and a more urban population. Mortality was exacerbated by high
HIV prevalence. The stringency and timing of government restrictions on
behaviour were not associated with a lower per capita mortality rate. A more
urban population and a higher infectious disease resilience score were
associated with more stringent restrictions and/or a higher per capita mortality
rate. The predictor set for the first and second waves were similar, and first
wave per capita mortality was a significant predictor of second wave per capita
mortality.
In summary, studies in this thesis showed that there were variations in
predictors of discovery both between virus types and geographical regions,
and identified high-risk regions for virus discovery beyond their historical extent.
The studies also provided proof-of-principle for the prediction of attributes such
as mortality, geographical extent, and disappearance for new human-infective
RNA viruses. These results help identify priority regions for investment in
surveillance systems for new human-infective viruses, and to make risk
assessments once they have emerged
Epidemiology of carbapenemase-producing organisms (CPO) in Scotland
No full textThe emergence and spread of carbapenem-resistant organisms (CRO) is a global public health threat in healthcare settings, resulting in high mortality, prolonged healthcare and increased costs. In the last two decades, many papers aiming to identify individuals at high risk of acquiring CRO have been published. However, the results reported across these studies are inconsistent and there are no studies systematically summarising those findings. Carbapenem resistance is mediated by multiple mechanisms. Carbapenemase production is the most concerning as the encoding genes of carbapenemases are located on mobile genetic elements, facilitating horizontal genetic exchange and therefore promoting the acquisition and spread of resistance genes. Examination of the epidemiology of carbapenemase-producing organisms (CPO) will inform local infection prevention and control strategies.
This thesis has two main parts. The aim of the first part is to systematically summarise risk factors for CRO infection and colonisation in healthcare facilities worldwide and identify study characteristics contributing most to the heterogeneity across studies. In the second part I focused on CPO in Scotland to investigate the incidence, microbiological characteristics and outcomes of CPO and determine risk factors associated with CPO among hospitalised patients.
In the first part, I conducted a systematic review and meta-analysis to evaluate risk factors associated with infection and/or colonisation of CRO in healthcare facilities. In total, 227 papers published between 1986 and 2016 were identified. Using pooled odds ratio estimates and the likelihood of statistical significance as criteria, prior carriage of multidrug-resistant organisms, prior antibiotics usage (carbapenem or oxazolidinone), prior provision of medical devices (mechanical ventilation or nasogastric tube) and prior healthcare exposure (intensive care unit ICU stay, and longer hospital stay) were most consistently found to be leading risk factors for CRO infection and/or colonisation. Additionally, decubitus ulcer was a specific leading risk factor for CRO infection, and prior antibiotics usage (polymyxin or cefepime) and steroid treatment were specific for hospital acquired CRO infection. However, prior provision of some medical devices (parenteral nutrition or gastrostomy or urinary catheter) were only leading risk factors for CRO colonisation. Study organism, case-control selection, study population, sample size, study setting and specialty (ICU or non-ICU) were the characteristics accounting for most heterogeneity across the published studies examined.
In the second part of this thesis, I focused on CPO in Scotland using data extracted from several national datasets. I performed a retrospective analysis on all CPO from clinical and screening cultures in 2003-2016 using generalised linear models and survival analyses, and then conducted a matched casecontrol study to determine risk factors for CPO infection and colonisation among hospitalised patients using conditional logistic regression models. In total, 243 CPO isolates were identified in 214 individuals from 13 of 14 NHS Boards. The overall incidence of CPO cases increased significantly (P<0.001), from 0.02 to 1.38 per 100,000 population. The case fatality rate was 5.6%. Enterobacteriaceae isolates predominated (84.8%) and increased significantly faster than non-fermenters. Community-associated CPO were more likely to be colonisations while healthcare-associated CPO were more likely to be infections. The ‘big 5’ carbapenemases (VIM, NDM, KPC, OXA-48 and IMP) predominated (96.7%). Awareness is required that older patients, with systemic infection or organ failure or presenting non-fermenters are at higher 30-day mortality risk from CPO. Patients with CPO infection had higher hospital mortality and longer hospital stay. A history of prolonged hospitalisation, prolonged ICU or high dependency unit (HDU) stay and being immunocompromised all independently increased the risk of CPO infection, while a history of HDU stay and ‘endocrine, nutritional and metabolic diseases’ were independent risk factors for CPO colonisation.
In conclusion, this thesis sheds light on patients at high risk of being infected or colonised by CRO including CPO in healthcare facilities. Pre-emptive management should be prioritised for these patients. The findings also demonstrate the necessity of continuing the existing acute hospital admission screening programme for carbapenemase-producing Enterobacteriaceae in Scotland. Future efforts are required to understand underlying factors accounted for mortality, evolution and transmission of carbapenem resistance in Scotland
Deep Inside the Blues with Margo Cooper, Joe Ayers & Trent Ayers
No full textPhotographer and author Margo Cooper will be joined in conversation by blues musicians Joe Ayers and his son Trent Ayers. Cooper had the privilege of interviewing both Ayers for her book Deep Inside the Blues. She describes Joe Ayers as kind, wise, and passionate about playing guitar. Trent Ayers grew up listening to a variety of blues music with his father—tapes of Arthur “Big Boy” Crudup, Muddy Waters, R. L. Burnside, and Junior Kimbrough. The father-son duo recently worked on an album together called A Father Son Legacy. Joe and Trent Ayers will play music during this SouthTalk. Margo Cooper’s recently published book, Deep Inside the Blues, is a collection of thirty-four interviews with blues artists and more than 160 of her photographs. Many of the key blues players of the period have already passed, making their stories and Cooper’s photographs of them all the more poignant and valuable. Holly Harris will facilitate conversation between the Ayers and Margo Cooper. Harris comes from a musical family, going back 5 generations. She is a veteran Blues radio DJ/producer, and emcee in the Boston area. She currently hosts SPINNING THE BLUES, on WUMB, live on Thursday and Saturday nights, and hosts KING ST BLUES online, on TGRN BLUES. Holly is the percussionist with The One Dime Band, plays at Juke Joint Fest in Clarksdale, and is a recipient of a W.C. Handy award for Commercial Radio. Harris is also a proud retired educator, and past president of the Boys and Girls Club of Greater Salem, MA
Data for "Pathogen transmission from vaccinated hosts can cause dose-dependent reduction in virulence"
No full text# Abstract # Many livestock and increasingly human vaccines are leaky, blocking symptoms without preventing infection or onward transmission. Leakiness is concerning as it increases vaccination coverage required to prevent disease spread, and can promote evolution of increased pathogen virulence. Despite leakiness, vaccination may reduce pathogen load, affecting disease transmission dynamics. However, the impacts on post-transmission disease development and infectiousness in contact individuals are unknown. Here, we use transmission experiments involving Marek’s disease virus in chickens to show that vaccination with a leaky vaccine substantially reduces viral load in both vaccinated individuals and unvaccinated contact individuals they infect. Consequently, contact birds are less likely to develop disease symptoms or die, show less severe symptoms when these are present, and shed less infectious virus themselves, when infected by vaccinated birds. These results highlight that even partial vaccination with a leaky vaccine can have unforeseen positive consequences in controlling the spread and symptoms of disease.Dunn, John R; Cheng, Hans H; Doeschl-Wilson, Andrea; Bailey, Richard I; Chase-Topping, Margo; Mays, Jody; Anacleto, Osvaldo. (2019). Data for "Transmission from vaccinated hosts can cause dose-dependent reduction in pathogen virulence", [dataset]. University of Edinburgh. https://doi.org/10.7488/ds/2725
Previously titled - Data for "Transmission from vaccinated hosts can cause dose-dependent reduction in pathogen virulence"
No full text# Abstract #
Many livestock and increasingly human vaccines are leaky, blocking symptoms without preventing infection or onward transmission. Leakiness is concerning as it increases vaccination coverage required to prevent disease spread, and can promote evolution of increased pathogen virulence. Despite leakiness, vaccination may reduce pathogen load, affecting disease transmission dynamics. However, the impacts on post-transmission disease development and infectiousness in contact individuals are unknown. Here, we use transmission experiments involving Marek’s disease virus in chickens to show that vaccination with a leaky vaccine substantially reduces viral load in both vaccinated individuals and unvaccinated contact individuals they infect. Consequently, contact birds are less likely to develop disease symptoms or die, show less severe symptoms when these are present, and shed less infectious virus themselves, when infected by vaccinated birds. These results highlight that even partial vaccination with a leaky vaccine can have unforeseen positive consequences in controlling the spread and symptoms of disease.* "MD_analysis_data_filtering_details.R" R code file identifying which datasets used for which analyses, and describing pre-analysis filtering.
* "Contact_2018.csv"
* "ContactDiseaseS_2018.csv"
* "ContactDiseaseSEM_2018.csv"
* "ContactInfection_2018.csv"
* "ContactMort_2018.csv"
* "HVT_qPCR_summary_RB18Nov2019.csv" Vaccine virus transmission qPCR results.
* "Shedder_2018.csv"
* "ViralLoadFile_2017_2018.csv
Epidemiology of MRSA in Scotland
No full textStaphylococcus aureus (S. aureus) is a bacterium that commonly colonises the skin
and nares of around one third of otherwise healthy individuals. While colonisation is
benign, S. aureus can cross skin and mucosal barriers to cause infections that
manifest as clinical disease. Clinical outcomes are diverse and range from mild, non-complicated
and often self-limiting skin and soft tissue infections (including boils,
abscesses and cellulitis) to more severe and life-threatening conditions including
pneumonia, toxic shock syndrome and bacteraemia. Medication isn’t always needed
for mild S. aureus infections as often they resolve with time but, for severe or
persistent cases, antimicrobial treatment is generally required. Following decades of
widespread and intensive usage of topical, enteral and parenteral antimicrobials to
treat S. aureus infections; AMR has become an established and ubiquitous problem
in the treatment of infections caused by this microorganism, especially when in the
methicillin resistant form (i.e. MRSA).
The aim of this thesis was to examine aspects of S. aureus epidemiology (including
MRSA and methicillin-sensitive S. aureus (MSSA)) in Scotland using statistical
methods and data from several large public health databases. More specifically this
involved: descriptions of spatial and temporal trends of morbidity and mortality;
comparisons of epidemiological and molecular attributes (including antimicrobial
resistance) of (1) MSSA and MRSA, and (2) the dominant clones of MRSA (i.e.
EMRSA-15 and EMRSA-16); descriptions of spatial and temporal trends of
antimicrobial prescribing in primary and secondary care and any associations
between prescribing rates and MRSA antimicrobial resistance; and carrying out a
hospital-level risk factor analysis of MRSA, testing hypotheses that hospital size,
hospital connectivity (through shared transfer patients) and hospital category have an
effect on hospital-level incidences of MRSA in mainland Scottish hospitals.
Results showed that total S .aureus bacteraemia and MRSA bacteraemia in Scotland
statistically declined over time (p0.05).
While combined mortality rates (i.e. all MSSA deaths (both primary and secondary
cause), or all MRSA deaths (both primary and secondary cause)) mirror these
findings; case-fatality ratios (CFR) show no declines over time for either MRSA or
MSSA. Results also show that several epidemiological factors point towards a
predominant community source for MSSA isolates (i.e. outside healthcare) and
hospital source for MRSA. Evidence for this included: (1) the lack of resistance
genes in the MSSA population, (2) MRSA was more associated with long-term care
and high-risk patients in the specialties care of the elderly, high dependency units
/intensive care units (HDU/ICU), and surgery and conversely MSSA with specialties
that commonly served outpatients, and (3) the abundance of non-EMRSA-15/non-
EMRSA-16 ‘other’ clones in the MSSA population as compared with the hospital-associated
CC22 (EMRSA-15) and CC30 (EMRSA-16) clones. EMRSA-15 was by
far the most dominant MRSA clone in Scotland with EMRSA-16 declining
significantly and non-EMRSA-15/non-EMRSA-16 clones causing an increasing
number of infections (over the time period 2003-2013). EMRSA-16 was resistant to
a larger number of antimicrobials than EMRSA-15, typically 9 versus 5, and while
resistance varied for EMRSA-16 over the study period, resistance remained stable
for EMRSA-15. There was little difference between clinical and screening MRSA
isolates. Analyses of antimicrobial prescribing showed that prescribing rates of
several drugs increased over time (2003-2013). Prescribing was far higher in primary
care settings than in secondary care, although this differed between antimicrobials.
Significant positive associations between prescribing and resistance rates were found
for gentamicin (pr - p<0.0001, se - p<0.0001) and trimethoprim (pr - p<0.01, se -
p<0.0001) in both primary (pr) and secondary (se) care, and clindamycin (p<0.0001)
in primary care only. Finally, in Scotland there is a threshold of connectivity above
which the majority of hospitals, regardless of size, are positive for MRSA. Higher
levels of MRSA are associated with the large, highly connected teaching hospitals
with high ratios of patients to domestic staff.
While there were a number of data limitations, this body of work provides a better
understanding of the epidemiology of S. aureus including MRSA in Scotland
PERILAKU KONSUMTIF PADA REMAJA STUDI DESKRIPTIF DI MALL MARGO CITY
No full textPenelitian ini bertujuan untuk memperdalam Perilaku Konsumtif Remaja Pasca Keberadaan Mall Rw 19 Kelurahan Kemiri Muka Kecamatan Beji Kota Depok. Penulis menggunakan metode deskriptif kualitatif dengan Teknik wawancara yaitu metode yang berupaya memecahkan dan menjawab permasalahan yang dihadapi pada saat ini. Tujuan utama untuk membuat penggambaran tentang suatu keadaan secara objektif. Penulis menggunakan perilaku konsumtif remaja baik faktor internal yakni motivasi, harga diri, pengamatan, kepribadian dan faktor eksternal yakni kebudayaan, kelas sosial, kelompok sosial, kelompok referensi, dan keluarga serta perilaku konsumtif yang berdasarkan pembelian impulsive, pemborosan dan pembelian tidak rasional. Pada penelitian ini digambarkan secara tepat kemudian diikuti oleh analisis menggunakan Teknik wawancara. Dari hasil tersebut, maka dapat diinterpretasikan bahwa, secara umum Perilaku Konsumtif Remaja Pasca Keberadaan Mall Margo City Rw 19 Kelurahan Kemiri Muka Kecamatan Beji Kota Depok ada 11 narasumber: bapak Widodo dan 10 anak remaja. Dari hasil analisis wawancara dapat diartikan bahwa perilaku konsumtif ini dapat dipahami serta diterapkan agar dapat menambah wawasan pengetahuan bagi peneliti tentang kondisi perilaku konsumtif remaja setelah keberadaan Margo City serta berkontribusi dalam memberikan dampak perubahan serta pengembangan ilmu pengetahuan khususnya perilaku konsumtif remaja pasca keberadaan mall
Kata Kunci : Perilaku Konsumtif, Remaja, Mall Margo City
This study aims to deepen the Consumptive Behavior of Adolescents After the Existence of Mall Rw 19, Kemiri Muka Village, Beji District, Depok City. The author uses a qualitative descriptive method with an interview technique, namely a method that seeks to solve and answer the problemfaced at this time. The main purpose is to make a description of a situation objectively. The author uses adolescent consumptive behavior both internal factors, namely motivation, self-esteem, observation, personality and external factors, namely culture, social class, social groups, reference groups, and family as well as consumptive behavior based on impulsive purchases, waste and irrational purchases. In this study described precisely then followed by analysis using interview techniques. From these results, it can be interpreted that, in general, the consumer behavior of adolescents after the existence of Margo City Mall Rw 19, Kemiri Muka Village, Beji District, Depok City, there were 11 sources: Mr. Widodo and 10 teenagers. From the results of the interview analysis, it can be interpreted that this consumptive behavior can be understood and applied in order to be able to add insight to the knowledge of researchers about the conditions of adolescent consumptive behavior after the existence of Margo City and to contribute to the impact of changes and the development of knowledge, especially adolescent consumptive behavior after the existence of the mall and can provide information to adolescents.
Keywords: Consumptive Behavior, Adolescents, Margo City Mal
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