185 research outputs found
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Microbial Diversity: Form and Function in Prokaryotes
No full textThis book offers the first comprehensive, in-depth treatment of microbial diversity for undergraduate and graduate students. Using a global approach, Microbial Diversity illustrates the impact of microorganisms on ecological and Earth system phenomena. Accompanied by a devoted website with resources for both instructors and students: www.blackwellpublishing.com/ogunseitan Uses key ecological and global phenomena to show the continuity of microbial contribution. Illustrates the importance of microbial diversity for the understanding of global physiochemical and biological processes. Presents analyses of microscopic, culture, molecular, and phylogenetic systematic methods. Shows the relevance of microbial diversity to global environmental problems, such as climate change and ozone depletion. Features numerous illustrations, including over 60 4-color photographs of microbes
Environmental proteomics: A long march in the pedosphere
No full textEnvironmental proteomics, the study of the expression profile of proteins extracted directly from living organisms and some stabilized extracellular proteins present in environmental samples, is a developing branch of soil science since the seminal papers appeared twenty years ago. Soil microbial communities hold the key to understanding terrestrial biodiversity; they are extremely complex and their physiological responses to dynamic environmental parameters are under-characterized. Therefore, the slow development of environment-related proteomic databases, and the high chemical reactivity of environmental matrices hamper the extraction, quantification, and characterization of proteins; and soil proteomics remains still in its infancy. We underscore the main achievements of environmental proteomics focusing on soil ecosystems, and we identify technical gaps that need to be bridged in the context of relevant ecological concepts that have received little attention in the development of proteomics methods. This analysis offers a new framework of research of soil proteomics toward improved understanding of the causal linkages between the structure and function of the soil microbiome, and a broader grasp of the sensitivity of terrestrial ecosystems to environmental change
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Antibiotic Stewardship in Ghana’s Global Health Security Agenda: A Cross-sectoral Assessment of Knowledge Translation into Practice
No full textBackground: Resistance of bacterial pathogens to antibiotic therapy threatens to derail progress made to reduce the global burden of infectious diseases, with the largest impact in countries such as Ghana where populations are vulnerable to pathogenic exposures. However, the level of antibiotic use and knowledge about antibiotic resistance among communities is inadequately quantified. This research aimed to identify gaps and priorities for strategies to improve antibiotic stewardship. Methods: A cross-sectional study of four hundred individuals residing in the urban Greater Accra and rural Upper West regions of Ghana was conducted to investigate knowledge, attitudes, and practices regarding antibiotics and antibiotic resistance. The determinants of antibiotic stewardship were assessed through associations between level of knowledge, attitudes, and utilization behaviors and demographic characteristics. Principal component and regression analyses were conducted to determine the different dimensions of knowledge and their association with antibiotic use. Eight semi-structured in-depth interviews with key personnel from the policy, research, and practice programs in Ghana’s public health sector were conducted to investigate stakeholder roles and institutional capacity to promote prudent use of antibiotics at the community level. Results: The results revealed that 70% of study participants (278/400) had used at least one antibiotic in the year prior to the survey. The most frequently used antibiotics were Amoxicillin, Amoxicillin-clavulanic acid, Ampicillin, Ciprofloxacin, and Metronidazole. Women and older adults had higher knowledge compared to their respective counterparts (p < 0.01). Prudent antibiotic use was significantly more prevalent in women than in men (p < 0.05). Most participants (63%) were unaware of antibiotic resistance. The determinants of antibiotic stewardship revealed two main principal components: knowledge about treatment of common illnesses showed that women and older individuals had higher knowledge about appropriate therapies for malaria, headaches, and body aches; and knowledge about prudent use of antibiotics indicated better knowledge about prudent use of antibiotics among older adults, persons with higher educational attainment, and residents of the Greater Accra region. Stakeholder analysis revealed four themes: national burden of disease and antibiotic resistance; policy development; implementation barriers; and strategies. All respondents expressed concern about the increasing proliferation of antibiotic-resistant bacteria, which they attributed in part to the inappropriate use of antibiotics in communities. Stakeholders acknowledged the importance of strengthening cross-sectoral collaboration, and the need to leverage resources from the animal and environmental sectors through a One Health approach. Conclusion: Findings from my research can improve knowledge about the public’s understanding of antibiotic resistance to better inform implementation of the Global Action Plan on Antimicrobial Resistance, particularly in low-resource settings
The Basel Convention and e-waste: translation of scientific uncertainty to protective policy
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Mixed-Method Analyses of Climate Change, Episodic Drought, and Vulnerability to Valley Fever Outbreaks in California
No full textCoccidioidomycosis (Valley Fever) incidence has been steadily increasing in the Southwest United States. In 2017, the highest record number of cases were diagnosed in the state of California, surpassing the previous record in 2016 by 34%, sparking a renewed interest in what is bringing about this increase in incident case counts. Coccidioides species of fungi grow in the soil and when the spores become aerosolized, they can be inhaled leading to infection. Previous studies have tried to understand the relationship between Valley Fever exposure and climate. The goal of this research is to understand the relationship between climate and Valley Fever and how this information can assist local public health agencies in communicating preventive strategies to the vulnerable populations in their local communities. The main research hypothesis is that the relationship with the climate variables and incidence will not behave identically in terms of direction or timing across the study area, except for Precipitation, which is hypothesized to have a positive relationship with cases over the Fall and Winter months. Monthly case data was obtained from the California Department of Public Health, Infectious Disease Branch, for five California Counties (Study area: Fresno, Kern, Kings, San Luis Obispo, and Tulare) for 2000-2015 totaling over 37,000 incident cases. To determine how environmental factors (precipitation, temperature, wind speed, evapotranspiration, Palmer Drought Severity Index, Particulate Matter 2.5 and 10, and El Nino Southern Oscillation Index) were related to diagnosed cases, linear and Poisson regression were used to analyze case counts and incidence rate for 2000-2015. To determine how the relationship between environmental factors and Valley Fever cases changed due to different hypothesized exposure scenarios, ten different exposure scenarios were investigated. To determine how the local public health agencies currently or would like to use climate information in Valley Fever messages, a qualitative survey and interview to representatives from the Public Health agencies in the study area were conducted. This study verified previous findings that the more total season rainfall that occurs during the Fall and Winter season typically indicates that cases will be higher the following diagnosis season for each county in the study area. Secondly, the Palmer Drought Severity Index, found that the drier the soil was in the months before the peak diagnosis season, the more cases were likely to be diagnosed. Third, most of the cases were diagnosed during La Nina events, which usually indicates a drier weather environment over California. These patterns emerged with the different quantitative methods and the different exposure periods, where the other environmental variables did not have this same consistency. Lastly, the Public Health Agencies in the study area would like to see climate information tailored in a way to allow Behavior Adaptation messaging like bad air quality days or the risk level for the upcoming flu season
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Antimicrobial Resistance in Nursing Homes: Unraveling the Epidemiology and Prevention of Methicillin-Resistant Staphylococcus aureus and Candidozyma auris
No full textThis dissertation examines two critical multidrug-resistant pathogens that disproportionately affect nursing homes: methicillin-resistant Staphylococcus aureus (MRSA), an endemic bacterium, and Candidozyma auris, a rapidly emerging yeast. C. auris has been called the “fungal MRSA” due to its shared propensity to extensively colonize the skin and nose, shed profusely into the environment, and persist on surfaces, promoting both infection risk and spread to others. While established prevention strategies exist for MRSA, effective measures for C. auris are lacking. To address this gap, this research compares MRSA and C. auris predisposition and prevention by 1) investigating the extent to which MRSA and C. auris share common risk factors for carriage and mechanisms of transmission and 2) assessing the adaptability of MRSA prevention strategies—such as antiseptic bathing and nasal decolonization—for C. auris control. Together, this work generates novel epidemiologic and microbiologic data uncovering the similarities and differences in MRSA and C. auris carriage, transmission, and prevention. Findings provide encouraging evidence that skin and nasal decolonization can effectively reduce C. auris burden in nursing homes, offering a practical approach to mitigate this emerging and urgent healthcare threat
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Preventive Strategies to Reduce Malaria Burden: Epidemiological Surveillance and Modeling for New Control and Elimination Methodologies
No full textMalaria epidemiology around the world is changing at a rapid pace due to intensive malaria control campaigns in the past decade. In spite of major progress in malaria control, new strategies are needed to reduce the malaria disease burden and reach global eradication goals. Within the framework of translational medicine, this interdisciplinary dissertation used a multilevel approach to describe and evaluate strategies seen as imperative to achieving the goal of malaria elimination set forth by the World Health Organization. We used a combination of field surveys and mathematical modeling methodologies to examine malaria epidemiology from the individual, the community, and the bench-side perspectives in countries aiming at control (Kenya) and elimination (Thailand). In Kenya, the combination of consumer, healthcare provider, and pharmaceutical retailer surveys revealed that the high cost of diagnosis and treatment at a healthcare facility may be inhibiting positive health-seeking behavior and may be incongruent with the goals ofxiiicurrent subsidization policies. In Thailand, field surveys identified cross-border human movement patterns and important migration parameters between Thailand and Myanmar. The multi-node model simulations found an indirect impact of interventions on the side of the border that did not receive the intervention. Sensitivity analyses showed that the indirect impact of vector control was stronger with increased migration rates. Therefore, in this border region that harbors a constant and unmonitored flow of people, the regional malaria elimination strategies need to be accommodative of highly mobile populations. Lastly, we used a combination of field survey data from Kenya and the mathematical model to explore potential added benefits of including a long-lasting microbial larvicide as a supplemental vector control strategy in endemic regions of sub-Saharan Africa where insecticide resistance and changes in vector behavior present significant challenges to control. The model results indicated that larviciding has the potential to provide significant added benefits to malaria control in the context of prevailing pyrethroid resistance and outdoor transmission. In conclusion, parameterizing mathematical models with field-derived entomological and epidemiological data framed within individual, community, and bench-side perspectives, can represent a valuable approach to assist malaria control and elimination efforts
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Inter-facility Patient Sharing and the Spread of Carbapenem-resistant Enterobacteriaceae
No full textCarbapenem-resistant Enterobacteriaceae (CRE) are a rapidly emerging group of multiple drug-resistant organisms (MDROs), with a mortality rate reaching 50\%, causing the CDC to declare them to be the highest level antibiotic-resistant microorganism threat. Drug resistance limits the available treatments for CRE to older, more toxic antibiotics and makes infection control practices to stop the spread of CRE crucial. Because of its dependence on human factors, the spread of MDROs was examined using a newly proposed social ecological model of CRE epidemiology which considered how factors at three levels - the patient, the hospital, and the nursing home - interact throughout inter-facility patient sharing to influence individual patient carriage of MDROs. The current research began necessary CRE surveillance by quantifying the current prevalence of CRE and identifying targets for intervention in a region in which CRE is still emerging. The results confirm the importance of containing CRE, which had a high mortality rate (31%) and extensive spread (52 days of healthcare facility exposure per year of follow up for CRE carriers). The results also suggest targets for intervention at the intra-personal level, including high comorbidity; and at the institutional levels, highlighting nursing home facilities. The results of statewide studies show that Southern California UC hospitals having 10 times the rate of CRE carriage than Northern California hospitals. Statewide results reaffirmed the high mortality rate and extensive healthcare facility exposure of CRE carriers, which were significantly greater than those of non-CRE carriers. They also emphasized the importance of surveillance definitions in the control of infectious disease and demonstrated how the intra-personal factor of the co-colonization among CRE carriers affects the potential impacts of institutional level contact precautions policies in preventing the spread of emerging MDROs. Understanding the interplay of factors at the intrapersonal and institutional levels that amplify MDRO spread is important to effectively target interventions, such as contact precautions, to reduce the burden of emerging MDROs. As the population in the United States ages, it will be increasingly important to understand how infection prevention policies at nursing home facilities and healthcare facility exposure contribute to the population burden of infectious disease
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Potential Exposure to Halogenated Flame-retardant Chemicals from Electronics in Academic Environments
No full textHalogenated flame-retardants are chemical compounds added to consumer products to delay fire ignition. Research studies have shown potential effects on human health, including ill effects on neurodevelopment. Therefore, it is important to investigate environmental scenarios that contribute to human exposure. Most exposure assessment studies regarding flame-retardants sample dust from the floor of the home only and assume 24 hours spent at home. To address current knowledge gaps, I investigated 10 microenvironments on the University of California, Irvine campus by collecting dust from elevated surfaces (ESD) and floors (FD). I measured concentrations of the following flame-retardant chemicals in each type of dust collection and across microenvironments: polybrominated diphenyl ether (PBDE) congeners were BDE-28, BDE-47, BDE-66, BDE-85, BDE-99, BDE-100, BDE-153, BDE-154, BDE-183, BDE-206, BDE-209 and the non-PBDEs were EH-TBB, BEH-TEBP, BTBPE, DBDPE, HBCD, TCEP, TCIPP, TDCIPP, and TBBPA. Secondly, I collected time activity diaries and estimated external flame-retardant exposure for individuals (N = 43) based on time spent across microenvironments and using ESD and FD chemical exposure estimates. Thirdly, I used a one-compartment pharmacokinetic model to estimate individual internal dose following exposure for the flame-retardant chemicals: BDE-28, BDE-47, BDE-99, BDE-100, BDE-153, BDE-154, BDE-183, BDE-209. Finally, I used meta-analysis of epidemiological studies on the association between the flame-retardant BDE-47 and infant motor development to estimate benchmark doses. The results are as follows: the ESD was statistically significantly higher than FD for 5 PBDEs and 3 non-PBDEs; estimates of human exposure to most chemicals through ESD are statistically significantly higher for ∑PBDE and ∑non-PBDEs than through FD; the body burden estimates were statistically significantly higher from ESD compared to FD; and 1%, 5%, and 10% benchmark doses for BDE-47 are 43.01, 1083, 61050 ng/g lipid of BDE-47, respectively. The conclusions are that estimates assuming continuous unidimensional exposure likely underestimate flame-retardant exposure and benchmark doses for BDE-47 that use human data are much higher than the reference dose based on animal data and uncertainty factors. The implications of this research are that exposure estimates made with FD may underestimate exposure and reference doses may overestimate risk
Tundra Soil Viruses Mediate Responses of Microbial Communities to Climate Warming
No full textABSTRACT The rise of global temperature causes the degradation of the substantial reserves of carbon (C) stored in tundra soils, in which microbial processes play critical roles. Viruses are known to influence the soil C cycle by encoding auxiliary metabolic genes and infecting key microorganisms, but their regulation of microbial communities under climate warming remains unexplored. In this study, we evaluated the responses of viral communities for about 5 years of experimental warming at two depths (15 to 25 cm and 45 to 55 cm) in the Alaskan permafrost region. Our results showed that the viral community and functional gene composition and abundances (including viral functional genes related to replication, structure, infection, and lysis) were significantly influenced by environmental conditions such as total nitrogen (N), total C, and soil thawing duration. Although long-term warming did not impact the viral community composition at the two depths, some glycoside hydrolases encoded by viruses were more abundant at both depths of the warmed plots. With the continuous reduction of total C, viruses may alleviate methane release by altering infection strategies on methanogens. Importantly, viruses can adopt lysogenic and lytic lifestyles to manipulate microbial communities at different soil depths, respectively, which could be one of the major factors causing the differences in microbial responses to warming. This study provides a new ecological perspective on how viruses regulate the responses of microbes to warming at community and functional scales. IMPORTANCE Permafrost thawing causes microbial release of greenhouse gases, exacerbating climate warming. Some previous studies examined the responses of the microbial communities and functions to warming in permafrost region, but the roles of viruses in mediating the responses of microbial communities to warming are poorly understood. This study revealed that warming induced changes in some viral functional classes and in the virus/microbe ratios for specific lineages, which might influence the entire microbial community. Furthermore, differences in viral communities and functions, along with soil depths, are important factors influencing microbial responses to warming. Collectively, our study revealed the regulation of microbial communities by viruses and demonstrated the importance of viruses in the microbial ecology research
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