Thesis (M Med.(Community Health))--University of Limpopo, 2009. / The threat posed by infectious diseases is progressively growing on a global scale. With 2010 rapidly approaching, when South Africa will host the Soccer World Cup, there will be a massive influx of foreigners into the country. The purpose of the study was evaluate to the status of Gauteng tertiary academic hospitals with respect to outbreak response and, with the help of existing local and international policies and research, to develop a generic model that can be used by hospitals in developing outbreak response policies and standard operating procedures. Methods A descriptive cross-sectional survey using a semi-structured questionnaire was utilized to evaluate the preparedness of tertiary health care facilities in South Africa. The target population consisted of Clinical Directors, Senior Clinical Executives/ Medical Superintendents, Infection Control Nurses and / or Quality Assurance Managers and Infection Control Nurses. These categories of health professionals were targeted as they are normally delegated responsibility for outbreak response activities. Results Twelve tertiary academic hospitals were included in the survey and nine responded to the survey questionnaire giving a 75% response rate. Other significant findings were: • 71% of the responding hospitals had clear terms of reference for their response team. v • 43% of the responding hospitals had a functional preparedness and response strategy / plan for priority diseases. • The most frequent point of entry in the tertiary academic hospitals is the casualty / emergency unit, followed by the trauma and OPD areas • There are very few ‘protective environment wards’ and ‘airborne infection isolation rooms’ in Gauteng Province. • Only 15% of responding hospitals have infection control compatible ventilation and only 42% could manage a patient that requires quarantine in the casualty/ emergency unit area. Most hospitals did not have the capacity to quarantine large number of patients. The study has also illustrated that there is no model easily available, suitable for the South African context, that can be used by hospital management in facility specific planning for infectious disease outbreaks. Conclusions It can be concluded from the findings of this study that academic hospitals in Gauteng, as well as in other areas of South Africa, are not adequately prepared for the management of an infectious disease outbreak.

The Madden-Julian Oscillation (MJO) is the leading mode of tropical intraseasonal variability and has known links to modification of extratropical patterns. Spatial and temporal scale differences between the MJO and US tornadoes makes connecting the two difficult, but using tornado outbreaks (TO) that are typically synoptically evident helps close this gap. An assessment of TO probability was conducted for each of the eight Realtime Multivariate MJO index phases for each month. In addition, clusters of TOs were used to identify how the MJO’s extratropical response influences patterns that lead to outbreaks in the US. It was found, and in part, consistent with previous research, that the shifts in the jet stream and wave breaking over the Pacific that occur in response to the current location of the MJO convection and circulation anomalies contribute to changes in the mid-latitude flow that can produce TOs in the central and eastern US.

During 2010 and 2011, the Loreto region of Peru experienced a dengue outbreak of unprecedented magnitude and severity for the region. This outbreak coincided with the reappearance of dengue virus-2 (DENV-2) in Loreto after almost 8 years. Whole-genome sequence indicated that DENV-2 from the outbreak belonged to lineage II of the southeast Asian/American genotype and was most closely related to viruses circulating in Brazil during 2007 and 2008, whereas DENV-2 previously circulating in Loreto grouped with lineage I (DENV-2 strains circulating in South America since 1990). One amino acid substitution (NS5 A811V) in the 2010 and 2011 isolates resulted from positive selection. However, the 2010 and 2011 DENV-2 did not replicate to higher titers in monocyte-derived dendritic cells and did not infect or disseminate in a higher proportion of Aedes aegypti than DENV-2 isolates previously circulating in Loreto. These results suggest that factors other than enhanced viral replication played a role in the severity of this outbreak.

Antibiotic resistance is increasing worldwide, which is threatening the effectiveness of even the most potent and recent antibiotics. The successful treatment of disease is hampered due to the multidrug resistant (MDR) phenotype exhibited by the bacterial pathogens. Therefore, the aims of this thesis were to investigate MDR through several different approaches. Integrons are important contributors to the MDR profile of nosocomial isolates within Australia, therefore the incidence of integrons was assessed in a collection of 72 conjugative clinical plasmids isolated from E. coli, a cohort of 30 urinary tract infection (UTI) isolates and a cohort of four bacteria producing metallo-beta-lactamases (MBLs). Integrons were found in 63% (45/72) of the conjugative plasmids by polymerase chain reaction (PCR). Sequencing of gene cassette arrays revealed that cassettes of the dfr and aadA families were most common. Within the cohort of UTI bacteria, 37% (11/30) were positive for class 1 integrons, and the dfrA17-aadA5 gene cassette array was most common. The four MBL-producers contained the gene cassette blaIMP-4 found within a class 1 integron which was responsible for the MBL phenotype. An assay based on real-time PCR was also developed to measure the recombination activity of the integron integrase (IntI) enzymes. The existing method of IntI measurement, the in vivo conduction assay, was used as a basis for the development of the real-time PCR assay. Five 59-be from the gene cassettes aadB, orfA, sat2, dfrA1 and aacA4 were cloned as recognition sites used in the real-time PCR assay. IntI1 was the most active integrase and showed an activity of 2.31 ?? 10??-1 when recombining the aadB and orfA 59-be. The highest level of class 2 integrase activity was 2.00 ?? 10-1?? during recombination of the sat2 and dfrA1 59-be, while IntI3 showed its highest recombination frequency of 2.29 ?? 10-1?? when the aadB and orfA 59-be were used. Additionally, the real-time PCR assay was used assess the levels of IntI activity over time. Using this method, the level of recombination as time progressed remained stable at a level of 4.10 ?? 10-2????. MDR was also analysed in 37 Acinetobacter baumannii isolates which were collected from four hospitals in Sydney. Minimum inhibitory concentration (MIC) analysis to 25 antibiotics revealed that all isolates showed a reduced susceptibility to between five and 24 antibiotics. PCR was performed to detect the presence of resistance determinants. Class 1 integrons encoding resistance to aminoglycosides, antiseptics and disinfectants were found in 35 % (13/37) of the isolates. Aminoglycoside resistance genes including aphA1 (12/37), strA (1/37) and strB (22/39) were also found. Resistance to beta-lactams was also observed in all isolates, which correlated with the presence of the ampC and blaOXA-51-like genes. The insertion sequence ISAba1 which provides an alternative promoter leading to increased gene expression was found upstream of the ampC gene in 29 isolates; the same isolates also contained the identical insertion sequence upstream of the carbapenemase resistance gene blaOXA-23. These 29 isolates also possessed the tetracycline resistance gene tetB. All but one of these 29 isolates also contained the gene blaTEM-1. Resistance to quinolones and fluoroquinolones was attributed to the presence of a Ser83-Leu83 gyrA mutation present in 36 resistant isolates. Furthermore, a putative dihydrofolate resistance gene, folA, was found in all isolates. Repetitive extragenic palindromic PCR revealed the presence of seven clonal groups. Overall, this study demonstrated the widespread impact and dissemination of MDR within nosocomial settings in Australia. The use of new assays, such as the real-time PCR assay developed in this thesis, is essential to the understanding of dissemination of antibiotic resistance.

Introduction: Each year in the United States, Salmonella enterica infections cause an estimated 1.2 million illnesses that result in 19,000 hospitalizations and 390 deaths. Illnesses occur sporadically throughout the year, but might also occur as part of an outbreak. Outbreaks are most commonly linked to a food source, but contact with live animals can also result in human outbreaks of illness. Methods: Outbreaks of Salmonella reported to the Centers for Disease Control and Prevention through National Outbreak Reporting System (NORS) from 2009–2014 with a primary mode of transmission listed as animal contact or food were analyzed to characterize the demographics of zoonotic outbreaks and examine how they differ from foodborne outbreaks. Missing data for age or sex categories were recoded as age or sex unknown. Chi-square tests were conducted to compare proportions of categorical variables. Logistic regression was used to calculate odds ratios for age, sex, health outcomes and multistate exposure. Wilcoxon rank-sum tests were used to compare medians for outbreak size and duration. Analyses were conducted using SAS 9.3. Results: During 2009–2014, a total of 484 outbreaks were reported through NORS; of these, 99 (20.5%) resulted from Salmonella transmission through animal contact and 385 (79.5%) resulted from foodborne transmission. These outbreaks resulted in 3,604 (19.8%) and 13,568 (80.2%) illnesses, respectively. A higher proportion of outbreak-associated illnesses among children aged(15.2% vs. 1.4%, p Conclusions: Outbreaks of Salmonella resulting from animal contact frequently have characteristics that are distinct from food outbreaks. Findings are consistent with reports in the literature where young children are disproportionately affected by animal contact outbreaks. Animal contact outbreaks might have a higher proportion of hospitalizations, emergency room visits, and healthcare provider visits. Animal contact outbreaks might also be longer in duration and are more likely to be multistate. Future investigations of multistate Salmonella outbreaks that are consistent with these differences should collect epidemiologic information regarding animal exposures to determine if contact with animals resulted in the transmission of the outbreak.

The Cholera outbreak at Tiberias on the Sea of Galilee in Oct., 1918, that I am about to describe was of great importance from a military point of view. Consequently, the author and a bacteriologist, (Capt. A. Compton, R.A.M.C., O.C. 32 Mobile Laboratory) were dispatched to the scene of the outbreak in order to investigate the conditions and, in short, to adopt any measures possible to suppress the epidemic. The matter was of considerable urgency. Tiberias lay on the direct line of communication for troops operating in the Damascus area, and it was essential that all reinforcements and food supplies pass through the town. The hilly nature of the country, the arid soil, the daily extremes of temperature at that season of the year - for the days were hot and the nights bitterly cold - the deficient and defective water supply - all these factors had a bearing upon the health of the troops and the nature of the problem. Had Cholera spread at that critical period to any great extent it might have brought, what proved to be, one of the most brilliant feats in military history, to an untimely close.

Most cases of blastomycosis are sporadic and only nine outbreaks representing a total of 112 cases have previously been reported. Less than half of these have been culture proven cases. Outbreaks have previously occurred in North Carolina, Minnesota, Illinois, Wisconsin and Virginia. We report three culturally confirmed cases of blastomycosis from Elizabethton, Tennessee, who had onset of illness within a one-week span of time. The patients presented with fever, chest pain, weight loss, poor appetite and myalgia. Each initially had a dry cough which became productive of purulent sputum as the illness progressed. Mild hemoptysis occurred during each patient's course. Serologic testing by immunodiffusion and enzyme immunoassay were positive and testing by complement fixation was negative in each case. The diagnosis was made by histopathology on transbronchial biopsy or transthoracic needle aspiration material. Each patient improved on ketoconazole therapy.

A better understanding of the performance in precision of physical parameterizations in NWP models is necessary for improving forecasts of tornadic outbreaks. For this study, WRF simulations of tornadic outbreaks were run using configurations of three microphysics, three convective physics, and two PBL physics schemes. Each configuration was subjected to ten iterations of SKEBS. The means of the ten perturbation members of each parameterization configuration were bootstrapped for SB CAPE, SB CIN, and 0-3km SRH to find 95% confidence interval widths at each grid point. Maps of these spreads provided a spatial analysis of the uncertainty. Analyses on correlations and clusters were performed to determine how the configurations related spatially and in magnitude. These uncertainties were further bootstrapped to compare the mean of each configuration in boxplots. The effect on the uncertainty produced by each configuration varied according to the diagnostic variable being analyzed.

Introduction: Acute gastroenteritis is a common illness in humans. It has a high morbidity worldwide and in the United States (U.S); a sizeable mortality is reported in developing countries. Viruses are a common cause of acute gastroenteritis and noroviruses are the leading cause of non-bacterial gastroenteritis (1). Fomites play an important role in the infection cycle of norovirus. This study explored the comparability between a quantitative microbial risk assessment (QMRA) model to predict the probability of illness from norovirus due to environmental contamination with actual observed attack rates, the impact of appropriate cleaning procedures on fomites contamination, and the role of fomites in the transmission of norovirusMethod: Data from three different norovirus illness outbreaks occurring from 2004 to 2005 in Arizona in different venues were used. Questionnaires were used to determine demographics, symptoms associated with gastrointestinal illness, medical visits, and potential exposures such as food items consumed. When available, stool samples were collected from ill participants. Fomites samples were also gathered from the different venues; houseboats, college summer camp living spaces, and a restaurant. These samples were tested for norovirus using reverse transcriptase polymerase chain reaction (RT-PCR). Viral concentration on fomites was calculated using the most probable number methodology.Results: Norovirus was found on fomites from all three outbreaks. Improper cleaning of fomites increased the proportion of norovirus positive fomites from 40 percent to 70 percent in contrast, after cleaning and disinfection with 5000 mg/L free chloride, the proportion of norovirus positive fomites decreased to 33%. The predicted values from the quantitative microbial risk assessment model were consistent with the observed epidemiological attack rates.Conclusion: This study showed unequivocally that fomites play an important role in the transmission cycle of norovirus, and that improper cleaning and disinfection procedures only serve to spread the virus to previously uncontaminated fomites. In the case of outbreaks where people are not always available to answer questionnaires, QMRA should be considered as a worthwhile alternative to a full-scale epidemiological study.

joruiz@clinic.ub.es / Introduction: Bartonella bacilliformis is the etiological agent of Carrion’s disease, which is a neglected disease linked to people in low-socioeconomic populations in Andean valleys. An outbreak of B. bacilliformis was reported in a rural area of the Peruvian Amazon region. The aim of this study was to characterize this outbreak using molecular techniques. Methodology: Fifty-three blood samples from patients diagnosed with Carrion’s disease were analyzed by molecular tools, using both a Bartonella-specific polymerase chain reaction (PCR) and an universal PCR, both based on 16S rRNA gene amplification. Additional water samples from the area were also analyzed. Results: Unexpectedly, the samples were positive only when the universal PCR was used. Although environmental contamination cannot be ruled out, the results showed that Sphingomonas faeni was the possible causative agent of this outbreak, and that water was the most feasible infection source. Conclusions: Diagnosis by clinical criteria or microscopy may lead to misdiagnosis. There is a need to include molecular tools in the routine diagnosis of febrile syndromes, including Carrion’s disease.