Lee, Sung-Geun; Cho, Han-Gil; Paik, Soon-Young
Norovirus is a major cause of viral gastroenteritis and a common cause of foodborne and waterborne outbreaks. Norovirus outbreaks are responsible for economic losses, most notably to the public health and food industry field. Norovirus has characteristics such as low infectious dose, prolonged shedding period, strong stability, great diversity, and frequent genome mutations. Besides these characteristics, they are known for rapid and extensive spread in closed settings such as hospitals, hotels, and schools. Norovirus is well known as a major agent of food-poisoning in diverse settings in South Korea. For these reasons, nationwide surveillance for norovirus is active in both clinical and environmental settings in South Korea. Recent studies have reported the emergence of variants and novel recombinants of norovirus. In this review, we summarized studies on the molecular epidemiology and nationwide surveillance of norovirus in South Korea. This review will provide information for vaccine development and prediction of new emerging variants of norovirus in South Korea.
Park, Chan Soon; Ha, Kyoung Hwa; Kim, Hyeon Chang; Park, Sungha; Ihm, Sang Hyun; Lee, Hae Young
We investigated the association between socioeconomic status and hypertension in Korea, a country that has experienced a dynamic socioeconomic transition. We analyzed participants of a prospective cohort study-the Korean Genome and Epidemiology Study-enrolled between 2001 and 2003. We recruited 7,089 subjects who underwent a 4-year follow up till 2007. Education and income levels, which are important parameters for socioeconomic status, were stratified into 4 groups. Education level was defined as short (≤ 6 years), mid-short (7-9 years), mid-long (10-12 years), and long (≥ 12 years). Monthly income level was stratified as low (< 500,000 KRW), mid-low (500,000-1,499,999 KRW), mid-high (1,500,000-2,999,999 KRW) or high (≥ 3,000,000 KRW). At baseline, 2,805 subjects (39.5%) were diagnosed with hypertension. Education and income levels were inversely associated with the prevalence and incidence of hypertension (P < 0.001). In multivariate analysis, a shorter duration of education was significantly associated with a higher prevalence of hypertension (P < 0.001), but income level was not (P = 0.305). During the follow-up, 605 subjects (14.2%) were newly diagnosed with hypertension. In multivariate adjusted analysis, the hazard ratios (95% confidence interval) for incident hypertension across the longer education groups were 0.749 (0.544-1.032), 0.639 (0.462-0.884), and 0.583 (0.387-0.879), compared with the shortest education group. There was no significant association between incident hypertension and income across higher income groups: 0.988 (0.714-1.366), 0.780 (0.542-1.121), and 0.693 (0.454-1.056), compared with the lowest income group. In conclusion, education and income levels are associated with the prevalence and incidence of hypertension, but only education is an independent prognostic factor in Korea.
The Epidemiology and Genomics Research Program, in the National Cancer Institute's Division of Cancer Control and Population Sciences, funds research in human populations to understand the determinants of cancer occurrence and outcomes.
This page provides links to research resources, complied by the Epidemiology and Genomics Research Program, that may be of interest to genetic epidemiologists conducting cancer research, but is not exhaustive.
Biliary atresia (BA) is the major cause of cholestasis and the leading indication for liver transplantation (LT). However, the incidence of BA in Korea has not been reported. The aim of this study was to investigate the incidence and clinical outcomes of BA in Korea. We used the Korean universal health insurance database and extracted data regarding BA patients younger than 18 years of age admitted between 2011 and 2015. The incidence of BA was calculated by dividing the number of BA patients by the number of live births. Two hundred forty infants were newly diagnosed with BA. A total of 963 BA patients younger than 18 years of age were followed up for 5 years. The overall incidence of BA was 1.06 cases per 10,000 live births. The incidence of BA was 1.4 times higher for female patients than for male patients. Additionally, significant seasonal variation was observed; in particular, the incidence of BA was 2 times higher from June through August than from December through February. Congenital anomalies were found in 38 of 240 patients (15.8%). Congenital heart diseases were major associated congenital anomalies (6.3%). Several complications developed during the study period, including cholangitis (24.0%), varix (6.2%), and gastrointestinal bleeding (4.4%). Three hundred and one of the 963 BA patients under 18 years of age (31.3%) received LT for BA. The incidence of BA is higher in Korea than that in Western countries. We also report significant gender-associated differences and seasonal variation with respect to the incidence of BA. PMID:28244293
Kim, Kwang-Moon; Kim, Young Mo; Shim, Yoon-Sang; Kim, Kwang Hyun; Chang, Hyuck Soon; Choi, Jong Ouck; Rho, Young Soo; Kim, Min-Sik; Choi, Eun Chang; Choi, Geon; Sung, Myung-Whun; Kim, Sang-Yun; Lee, Yong-Sik; Baek, Jung-Hwan; Kim, Sang-Hyun; Kim, Young-Ho; Im, Jung-Hyuk; Choi, Sang-Hak; Kim, Jae-Hee
Head and neck cancers have never been systematically studied for clinical purposes yet in Korea. This epidemiological survey on head and neck cancer patients was undertaken from January to December 2001 in 79 otorhinolaryngology resident-training hospitals nationwide. The number of head and neck cancer patients was 1,063 cases in the year. The largest proportion of cases arose in the larynx, as many as 488 cases, which accounted for 45.9%. It was followed by, in order of frequency, oral cavity (16.5%), oropharynx (10.0%), and hypopharynx (9.5%). The male:female ratio was 5:1, and the mean age was 60.3 yr. Surgery was the predominant treatment modality in head and neck cancers: 204 (21.5%) cases were treated with only surgery, 198 (20.8%) cases were treated with surgery and radiotherapy, 207 cases (21.8%) were treated with combined therapy of surgery, radiotherapy, and chemotherapy. Larynx and hypopharynx cancers had a stronger relationship with smoking and alcohol drinking than other primary site cancers. Of them, 21 cases were found to be metastasized at the time of diagnosis into the lung, gastrointestinal tract, bone, or brain. Coexisting second primary malignancies were found in 23 cases. At the time of diagnosis, a total of 354 cases had cervical lymph node metastasis accounting for 42.0%.
Lee, Sunhee; Jang, Guehwan; Lee, Changhee
Porcine astrovirus (PAstV) is broadly distributed in pigs in several countries worldwide. PAstVs belong to the genus Mamastrovirus and are divided into five genetically divergent types. This study presents a molecular characterization of PAstV identified in diarrheic piglets in South Korea. The complete genome of the Korean PAstV strain KOR/KNU14-07/2014 was sequenced and analyzed to characterize PAstV circulating in South Korea. The full-length genomic sequence of KNU14-07 was determined to be 6,337 nucleotides in length and consisted of three major open reading frames (5'-ORF1a-ORF1b-ORF2-3'). The overall degree of nucleotide sequence identity was 40.8 to 72.5% between KUN14-07 and other reported PAstVs, indicating high heterogeneity among PAstVs. Genetic and phylogenetic analyses showed that the KNU14-07 strain was most closely related to the PAstV2 lineage, which is the second most common type in South Korea.
Park, Ji Young
Lung cancer causes the most cancer deaths in Korea. Although the smoking rate has begun to decrease, the prevalence of lung cancer is still increasing. We reviewed the national lung cancer registry data and the data published about lung cancer in Korea. In 2012, the crude incidence rate of lung cancer was 43.9 per 100,000. The age-standardized mortality rate of lung cancer was 19.8 per 100,000. The 5-year relative survival rate for lung cancer was 11.3% from 1993 to 1995 and increased to 21.9% in the period from 2008 to 2012. Lung cancer occurring in never-smokers was estimated to increase in Korea. Adenocarcinoma is steadily increasing in both women and men and has replaced squamous cell carcinoma as the most common type of lung cancer in Korea. In patients with adenocarcinoma, the frequency of EGFR mutations was 43% (range, 20%–56%), while that of the EMK4-ALK gene was less than 5%. PMID:27064578
Lee, Jung Hoon; Lim, Nam-Kyoo
Background and Objectives Heart failure (HF) is an important healthcare issue because of its high mortality, morbidity, and healthcare costs. The number of HF patients is increasing worldwide as a consequence of aging of the population. However, there are limited studies on the prevalence of HF in Korea. This study aimed to estimate the prevalence of HF, its comorbidities, and the projected population with HF in the future. Materials and Methods The prevalence and comorbidity estimates of HF were determined using data from the 2002-2013 National Sample Cohort based on the National Health Information Database. We calculated the projected prevalence of HF by multiplying the estimated prevalence in 2013 by the projected population counts for 2015-2040. Results The prevalence of HF in Korea was estimated to be 1.53% in 2013. The prevalence of HF in Korea is expected to increase by 2-fold, from 1.60% in 2015 to 3.35% in 2040. By 2040, more than 1.7 million Koreans are expected to have HF. In terms of comorbid diseases of HF, ischemic heart disease, hypertension, and diabetes mellitus were common (45.4%, 43.6%, and 49.1% in 2013, respectively). The prevalence rates of arrhythmia, valvular disease, and cardiomyopathy in HF patients were approximately 22.6%, 5.6%, and 3.1% in 2013, respectively. Conclusion This is the first nationwide report in Korea to demonstrate the prevalence and comorbidities of HF. These data may be used for the prevention and management of HF in Korea. PMID:27721857
Wang, Daxi; Young, Neil D; Koehler, Anson V; Tan, Patrick; Sohn, Woon-Mok; Korhonen, Pasi K; Gasser, Robin B
Clonorchiasis is a neglected tropical disease that affects >35 million people mainly in China, Vietnam, South Korea and some parts of Russia. The disease-causing agent, Clonorchis sinensis, is a liver fluke of humans and other piscivorous animals, and has a complex aquatic life cycle involving snails and fish intermediate hosts. Chronic infection in humans causes liver disease and associated complications including malignant bile duct cancer. Central to control and to understanding the epidemiology of this disease is knowledge of the specific identity of the causative agent as well as genetic variation within and among populations of this parasite. Although most published molecular studies seem to suggest that C. sinensis represents a single species and that genetic variation within the species is limited, karyotypic variation within C. sinensis among China, Korea (2n=56) and Russian Far East (2n=14) suggests that this taxon might contain sibling species. Here, we assessed and applied a deep sequencing-bioinformatic approach to sequence and define a reference mitochondrial (mt) genome for a particular isolate of C. sinensis from Korea (Cs-k2), to confirm its specific identity, and compared this mt genome with homologous data sets available for this species. Comparative analyses revealed consistency in the number and structure of genes as well as in the lengths of protein-coding genes, and limited genetic variation among isolates of C. sinensis. Phylogenetic analyses of amino acid sequences predicted from mt genes showed that representatives of C. sinensis clustered together, with absolute nodal support, to the exclusion of other liver fluke representatives, but sub-structuring within C. sinensis was not well supported. The plan now is to proceed with the sequencing, assembly and annotation of a high quality draft nuclear genome of this defined isolate (Cs-k2) as a basis for a detailed investigation of molecular variation within C. sinensis from disparate
This review assessed the epidemiology of voiding dysfunctions in South Korea. Comprehensive understanding of this epidemiology is crucial because the senior population and the social burden are increasing because of voiding dysfunctions is growing. We searched the medical records using several terms related to voiding dysfunction: benign prostatic hyperplasia, urinary incontinence, lower urinary tract symptoms, overactive bladder, and nocturia. We then estimated the prevalence of voiding dysfunctions in South Korea; our data were comparable with those from other countries, with slight differences. The ranges of incidences varied widely between studies, mostly because investigators defined disorders differently. Voiding dysfunction greatly affects healthcare costs and individual quality of life; therefore, more proper and valuable epidemiologic data are needed. In addition, efforts to unify the definitions of various voiding dysfunctions and progress in investigational methodologies using multimedia are warranted. PMID:27377940
Kim, June Myung; Cho, Goon Jae; Hong, Sung Kwan; Chang, Kyung Hee; Chung, Joo Sup; Choi, Young Hwa; Song, Young Goo; Huh, Aejung; Yeom, Joon Sup; Lee, Kkot Sil; Choi, Jun Yong
HIV infection/AIDS shows characteristic epidemiological and clinical patterns according to the region, country, and race. The epidemiological and clinical patterns of HIV infection/ AIDS in Korea was investigated by retrospectively analyzing the medical records of 176 HIV-infected persons who visited two major referral hospitals of AIDS in Korea from 1985 to April 2000. The most common transmission route was heterosexual contact (52.3%), followed by homosexual contact (23.9%). Among the opportunistic diseases, candidiasis was the most prevalent (21.6%), followed by Pneumocystis carinii pneumonia (15.9%), tuberculosis (12.5%), and CMV infection (9.1%). The most common initial AIDS-defining opportunistic disease was tuberculosis (33.3%). The most common causes of death were tuberculosis (25.7%) and Pneumocystis carinii pneumonia (25.7%). This study describes the epidemiological and clinical patterns of HIV infection/AIDS in Korea, which not only enables us to accurately understand HIV infection/ AIDS in this country, but eventually to aid in establishing effective preventive measures and treatment guidelines in Korea.
Lee, Changhwan; Ki, Moran
The recent outbreak of Middle East Respiratory Syndrome (MERS) coronavirus infection in Korea resulted in large socioeconomic losses. This provoked the Korean government and the general public to recognize the importance of having a well-established system against infectious diseases. Although epidemiologic investigation is one of the most important aspects of prevention, it has been pointed out that much needs to be improved in Korea. We review here the current status of the Korean epidemiologic service and suggest possible supplementation measures. We examine the current national preventive infrastructure, including human resources such as Epidemic Intelligence Service officers, its governmental management, and related policies. In addition, we describe the practical application of these resources to the recent MERS outbreak and the progress in preventive measures. The spread of MERS demonstrated that the general readiness for emerging infectious diseases in Korea is considerably low. We believe that it is essential to increase society's investment in disease prevention. Fostering public health personnel, legislating management policies, and establishing research centers for emerging infectious diseases are potential solutions. Evaluating international preventive systems, developing cooperative measures, and initiating improvements are necessary. We evaluated the Korean epidemiologic investigation system and the public preventive measures against infectious diseases in light of the recent MERS outbreak. We suggest that governmental authorities in Korea enforce preventive policies, foster the development of highly qualified personnel, and increase investment in the public health domain of infectious disease prevention.
Lee, Changhwan; Ki, Moran
The recent outbreak of Middle East Respiratory Syndrome (MERS) coronavirus infection in Korea resulted in large socioeconomic losses. This provoked the Korean government and the general public to recognize the importance of having a well-established system against infectious diseases. Although epidemiologic investigation is one of the most important aspects of prevention, it has been pointed out that much needs to be improved in Korea. We review here the current status of the Korean epidemiologic service and suggest possible supplementation measures. We examine the current national preventive infrastructure, including human resources such as Epidemic Intelligence Service officers, its governmental management, and related policies. In addition, we describe the practical application of these resources to the recent MERS outbreak and the progress in preventive measures. The spread of MERS demonstrated that the general readiness for emerging infectious diseases in Korea is considerably low. We believe that it is essential to increase society’s investment in disease prevention. Fostering public health personnel, legislating management policies, and establishing research centers for emerging infectious diseases are potential solutions. Evaluating international preventive systems, developing cooperative measures, and initiating improvements are necessary. We evaluated the Korean epidemiologic investigation system and the public preventive measures against infectious diseases in light of the recent MERS outbreak. We suggest that governmental authorities in Korea enforce preventive policies, foster the development of highly qualified personnel, and increase investment in the public health domain of infectious disease prevention. PMID:26493654
Moon, Shinje; Hong, Yeongseon; Hwang, Kyu-Jam; Kim, Suyeon; Eom, Jihye; Kwon, Donghyok; Park, Ji-Hyuk; Youn, Seung-Ki; Sohn, Aeree
Lyme borreliosis is one of the most common tick-borne infections in the northern hemisphere. However, the epidemiological features and clinical manifestations of this disease in Korea are unknown. The present study is the first to investigate the characteristics of Lyme borreliosis in Korea. We traced suspected cases of Lyme borreliosis during the period 2005-2012. Of the 16 identified patients with the disease, 11 had acquired autochthonous infection within Korea, while 5 patients were infected outside Korea. The history of past exposure was investigated in 8 of the 11 patients with autochthonous infection; 5 of these 8 patients (62.5%) were suspected to have acquired the infection in the northeastern alpine region. Clinically, of 11 patients with autochthonous infection, 6 (54.5%) showed early skin manifestations, 4 (36.4%) showed neurological manifestations, and 1 (9.1%) showed acrodermatitis chronica atrophicans. In conclusion, Lyme borreliosis could be endemic in the northeastern alpine region of Korea, and neurological and early skin manifestations are likely to be the major clinical characteristics of autochthonous Lyme borreliosis in Korea.
Kim, Suyeon; Chung, Han Young; Lee, Dong-Hoon; Lim, Jong Gyu; Kim, Se Keun; Ku, Hye-Jin; Kim, You-Tae; Kim, Heebal; Ryu, Sangryeol; Lee, Ju-Hoon; Choi, Sang Ho
Vibrio parahaemolyticus is a Gram-negative, motile, nonspore-forming pathogen that causes foodborne illness associated with the consumption of contaminated seafoods. Although many cases of foodborne outbreaks caused by V. parahaemolyticus have been reported, the genomes of only five strains have been completely sequenced and analyzed using bioinformatics. In order to characterize overall virulence factors and pathogenesis of V. parahaemolyticus associated with foodborne outbreak in South Korea, a new strain FORC_008 was isolated from flounder fish and its genome was completely sequenced. The genomic analysis revealed that the genome of FORC_008 consists of two circular DNA chromosomes of 3266 132 bp (chromosome I) and 1772 036 bp (chromosome II) with a GC content of 45.36% and 45.53%, respectively. The entire genome contains 4494 predicted open reading frames, 129 tRNAs and 31 rRNA genes. While the strain FORC_008 does not have genes encoding thermostable direct hemolysin (TDH) and TDH-related hemolysin (TRH), its genome encodes many other virulence factors including hemolysins, pathogenesis-associated secretion systems and iron acquisition systems, suggesting that it may be a potential pathogen. This report provides an extended understanding on V. parahaemolyticus in genomic level and would be helpful for rapid detection, epidemiological investigation and prevention of foodborne outbreak in South Korea.
Park, Sang-Ik; Jeong, Cheol; Kim, Ha-Hyun; Park, Sung-Hee; Park, Su-Jin; Hyun, Bang-Hun; Yang, Dong-Kun; Kim, Sang-Ki; Kang, Mun-Il; Cho, Kyoung-Oh
Since the prevalence of bovine norovirus (BNoV) and their genetic diversity have only been reported in the USA, England, Germany and The Netherlands, this study examined the prevalence and genetic diversity of BNoVs in diarrheic calves in South Korea using 645 diarrheic fecal specimens from calves by RT-PCR and nested PCR assays. Overall, 9.3% of the diarrheic fecal samples tested positive for BNoVs by either RT-PCR or nested PCR, of which 5.9% samples also tested positive for other enteric pathogens including the bovine coronavirus, bovine viral diarrhea virus, bovine torovirus, bovine groups A, B and C rotaviruses, bovine enteric Nebraska-like calicivirus and Escherichia coli. The genetic diversity was determined by direct sequencing of the partial RdRp region of 12 BNoVs detected from the fecal samples by nested PCR. Among the BNoVs examined, one Korean BNoV strain had the highest nucleotide (86.8%) and amino acid (99.1%) identity with the genotype 1 BNoV (GIII-1) strain, while the remaining 11 Korean BNoVs shared a higher nucleotide (88.0-90.5%) and amino acid (93.5-99.1%) identity with the genotype 2 BNoV (GIII-2) strains. The phylogenetic data for the nucleotide and amino acid sequences also demonstrated that one Korean BNoV strain clustered with GIII-1 but the remaining eleven strains clustered with GIII-2. In conclusion, BNoV infections are endemic and there are two distinct genotypes with GIII-2 being the main genotype circulating in the calf population in South Korea.
Epidemiology is the scientific study of the causes and distribution of disease in populations. NCI-funded epidemiology research is conducted through research at institutions in the United States and internationally.
The current epidemic of artemisinin resistant Plasmodium falciparum in Southeast Asia is the result of a soft selective sweep involving at least 20 independent kelch13 mutations. In a large global survey, we find that kelch13 mutations which cause resistance in Southeast Asia are present at low frequency in Africa. We show that African kelch13 mutations have originated locally, and that kelch13 shows a normal variation pattern relative to other genes in Africa, whereas in Southeast Asia there is a great excess of non-synonymous mutations, many of which cause radical amino-acid changes. Thus, kelch13 is not currently undergoing strong selection in Africa, despite a deep reservoir of variations that could potentially allow resistance to emerge rapidly. The practical implications are that public health surveillance for artemisinin resistance should not rely on kelch13 data alone, and interventions to prevent resistance must account for local evolutionary conditions, shown by genomic epidemiology to differ greatly between geographical regions. DOI: http://dx.doi.org/10.7554/eLife.08714.001 PMID:26943619
Yoo, Seok-Ju; Lee, Kwan
Objectives A salmonellosis outbreak occurred within a community of Gyeongju residents who ingested catered food from a wedding in June 2009. We aimed to epidemiologically investigate the probable vehicle of the infection. Methods We conducted a retrospective cohort study on 34 local residents who ingested the wedding food. Results Among the 34 residents, 31 (91.2%) reported symptoms of infection after eating the food. Among all of the wedding foods, pan-fried foods were highly associated with the diarrheal attack rate. On bacteriological examination, Salmonella species were detected in the pan-fried foods among the leftover foods and in 17 of the 31 stool specimens from the cases. There were five different types of pan-fried foods, but the onset of symptoms was independent of the ingredients used. We found that the pan-fried food was prepared at a food store in Seoul and that eggs were a common ingredient. Conclusions The major cause of the salmonellosis in this population was presumed to be the pan-fried food prepared with contaminated eggs. These food items might have been partially undercooked because of their irregular shape, which allowed the Salmonella species to survive and multiply before ingestion. PMID:24921021
Large-scale studies of genomic variation could assist efforts to eliminate malaria. But there are scientific, ethical and practical challenges to carrying out such studies in developing countries, where the burden of disease is greatest. The Malaria Genomic Epidemiology Network (MalariaGEN) is now working to overcome these obstacles, using a consortial approach that brings together researchers from 21 countries. PMID:19079050
Moon, Shinje; Kwak, Wooseok; Lee, Sangwon; Kim, Won; Oh, Jaeyeon; Youn, Seung-Ki
The first case of human cryptosporidiosis was reported in Korea in 1995; however, an outbreak of Cryptosporidium has not been reported in Korea until now. This paper describes the first outbreak of cryptosporidiosis in Korea. On May 24, 2012, a local public health center filed a report on 126 residents with gastrointestinal symptoms in an old apartment complex in Seoul. Epidemiological investigations were implemented on 125 of the 126 patients. The patients were reported continuously over a period of 22 days. Diarrhea was the most common clinical symptom, and lasted for 5 days on average. The tap water was the only common exposure of the patients. During the environmental investigation it was discovered that the water and septic tanks were situated closely and that the waste water pipes were corroded where they passed over the water pipes. Cryptosporidium parvum was detected in 3 of the 7 stool specimens by PCR-RFLP. A number of Cryptosporidium oocysts were also detected in the water specimens from the water tank. In conclusion, Cryptosporidium parvum was the key causal pathogen of this outbreak. It is presumed that the tap water was contaminated by a sewage leak from the aged pipelines.
Lee, Won-Chang; Kwon, Young Hwan
Background/Aims: To compare the epidemiological aspects of enterohemorrhagic Escherichia coli (EHEC) between Korea and Japan by analyzing the current state of EHEC infection outbreaks and related risk factors. Methods: We investigated the epidemiological aspects of EHEC infection cases between Korea and Japan from 2006 to 2010. The following factors were analyzed: national prevalence rate (PR), regional prevalence rate, epidemic aspects (i.e., Cases related to gender), male to female morbidity ratio, age, and seasonal distribution. Results: In total, there were 254 cases of EHEC with an average PR of 0.11 per 100,000 populations in Korea from 2006 to 2010. During the same period in Japan, there were 20,883 cases of EHEC with an average PR of 3.26 per 100,000 populations. The PR in Japan was significantly higher than that in Korea (p < 0.01). In both countries, more females than males had EHEC infections, with the highest incidence of infections (> 50%) observed for individuals younger than 9 years. EHEC is an emerging zoonosis and may be caused by consumption of raw or undercooked meat products from ruminants. Conclusions: This study provides a quantitative analysis of the epidemiological aspects and risk factors of EHEC infections in Korea and Japan and will provide insight on effective future strategies to reduce these infections. PMID:26886212
Tang, Patrick; Croxen, Matthew A; Hasan, Mohammad R; Hsiao, William W L; Hoang, Linda M
With the growing importance of infectious diseases in health care and communicable disease outbreaks garnering increasing attention, new technologies are playing a greater role in helping us prevent health care-associated infections and provide optimal public health. The microbiology laboratory has always played a large role in infection control by providing tools to identify, characterize, and track pathogens. Recently, advances in DNA sequencing technology have ushered in a new era of genomic epidemiology, where traditional molecular diagnostics and genotyping methods are being enhanced and even replaced by genomics-based methods to aid epidemiologic investigations of communicable diseases. The ability to analyze and compare entire pathogen genomes has allowed for unprecedented resolution into how and why infectious diseases spread. As these genomics-based methods continue to improve in speed, cost, and accuracy, they will be increasingly used to inform and guide infection control and public health practices.
Chung, You Nam; Park, Young Seok; Min, Kyung Soo; Lee, Mou Seop; Kim, Young Gyu
Objective The aim of the present study is to estimate the incidence trend of head injury and the mortality based on traffic accident statistics and to investigate the impacts of rapid industrialization and economic growth on epidemiology of head injury in Korea over the period 1970–2012 including both pre-industrialized and post-industrialized stages. Methods We collected data of head injury estimated from traffic accident statistics and seven hospital based reports to see incidence trends between 1970 and 2012. We also investigated the population structure and Gross National Income (GNI) per capita of Korea over the same period. The age specific data were investigated from 1992 to 2012. Results The incidence of head injury gradually rose in the 1970s and the 1980s but stabilized until the 1990s with transient rise and then started to decline slowly in the 2000s. The mortality grew until 1991 but gradually declined ever since. However, the old age groups showed rather slight increase in both rates. The degree of decrease in the mortality has been more rapid than the incidence on head injury. Conclusion In Korea during the low income stage, rapid industrialization cause considerable increase in the mortality and the incidence of head injury. During the high income stage, the incidence of head injury gradually declined and the mortality dropped more rapidly than the incidence due to preventive measures and satisfactory medical care. Nevertheless, the old age groups revealed rather slight increase in both rates owing to the large population structure and the declining birth rate. PMID:26962421
Lim, Seungmo; Zhao, Fumei; Yoo, Ran Hee; Igori, Davaajargal; Jeong, Jae Cheol; Lee, Haeng-Soon; Kwak, Sang-Soo
The complete genome sequence of a South Korean isolate of Rehmannia mosaic virus (ReMV) infecting Rehmannia glutinosa was determined through next-generation sequencing and Sanger sequencing. To our knowledge, this is the first report of a natural infection of R. glutinosa by ReMV in South Korea. PMID:26823577
Shin, Sang Heum; Roh, Hanseong; Kim, Juhyeok; Cho, Sukhyeong; Um, Youngsoon; Lee, Jinwon; Ryu, Yeon-Woo; Chong, Hyonyong; Yang, Kap-Seok
Here we report the full genome sequence of Klesiella oxytoca M1, isolated from Manripo area of South Korea. The strain K. oxytoca M1 is able to produce either 2,3-butanediol or acetoin selectively by controlling the pH and temperature.
Cho, Sang-Yun; Lim, Seungmo; Kim, Hongsup; Yi, Seung-In
We report here the first complete genome sequence of Ornithogalum mosaic virus (OrMV) isolated from Taean, South Korea, in 2011, which was obtained by next-generation sequencing and Sanger sequencing. The sequence information provided here may serve as a potential reference for other OrMV isolates. PMID:27516509
Han, Bok-Soon; Lee, Myeong-Jin; Kwon, Young-Hwan; Lee, Won-Chang
Background In the present study, we compared the epidemiological aspects of Legionnaire’ disease (LD) outbreaks in Korea and Japan by analyzing the current state from 2010 to 2014. Methods The following factors were analyzed: nationwide cumulative incidence rate (CIR) per 100,000 populations and case-fatality rate in percentage, epidemiological aspects (i.e., case related to gender), male to female morbidity ratio (MFMR), age, seasonality and habitat distribution of LD cases. Results In total, there were 134 cases of LD with the CIR of 0.05 per 100,000 populations in Korea from 2010 to 2014. During the same period in Japan, there were 4,840 cases of LD with a CIR of 0.76 per 100,000 populations. The CIR in Japan was significantly higher than that in Korea. However, the case-fatality rates were at similar levels (3.0% vs. 5.9%). Moreover, LD affects both sexes differently, accounting for 2.05 and 4.41 of MFMR in Korea and Japan, respectively. In both countries, the incidence mainly occurred among people aged 40 years or older, and peaked in summer (37.3% vs. 33.7% of total cases). Significant differences were observed in the incidence of LD cases between the capital city and county areas in both two countries. These differences in LD risk factors reflect the different influences of reservoir/host with natural or artificial aquatic environments. Conclusion This study provides a quantitative analysis of the epidemiological aspects and risk factors of LD outbreaks in Korea and Japan. We hope this study would be helpful for providing insight on effective future strategies to reduce LD outbreaks. PMID:27924178
Park, Sun-Whan; Ryou, Jungsang; Choi, Woo-Young; Han, Myung-Guk; Lee, Won-Ja
Since the first reported case of severe fever with thrombocytopenia syndrome (SFTS) in South Korea in 2013, between 2013 and 2015, we collected 1,697 serum samples from suspected patients who experienced symptoms of SFTS. We performed reverse transcriptase polymerase chain reaction using total RNA extracted from the patients' sera. When viral RNA was detected in the sera, SFTS was diagnosed. Among the 1,697 samples, 170 were positive for SFTS virus. We then analyzed the epidemiologic features of these 170 cases. As a result, we found that the annual number of cases increased steadily. However, the annual case fatality rate exhibited a downward trend. The majority of patients were aged ≥ 60 years, and most cases occurred during May–October in the eastern and southern parts of the country. These results may be useful for effective SFTS control by describing the clinical and epidemiologic features of the disease in South Korea. PMID:27928084
Bessen, Debra E.; McShan, W. Michael; Nguyen, Scott V.; Shetty, Amol; Agrawal, Sonia; Tettelin, Hervé
Streptococcus pyogenes (group A streptococcus; GAS) is a strict human pathogen with a very high prevalence worldwide. This review highlights the genetic organization of the species and the important ecological considerations that impact its evolution. Recent advances are presented on the topics of molecular epidemiology, population biology, molecular basis for genetic change, genome structure and genetic flux, phylogenomics and closely related streptococcal species, and the long- and short-term evolution of GAS. The application of whole genome sequence data to addressing key biological questions is discussed. PMID:25460818
Choi, Kang-Seuk; Lee, Eun-Kyoung; Jeon, Woo-Jin; Kwon, Jun-Hun; Lee, Jin-Hwa; Sung, Haan-Woo
A Newcastle disease surveillance program was conducted at live bird markets in Korea to expand our epidemiologic understanding of the disease in Korea. During the surveillance program, 10 lentogenic Newcastle disease viruses (NDVs) were isolated and identified from apparently healthy chickens and ducks at live bird markets. The lentogenic viruses had sequence motifs of either 112GKQGRL117 (n = 8) or 112GRQGRL117 (n = 2) at the F0 cleavage site. Sequencing and phylogenetic analyses of NDV isolates based on the hypervariable region of the F protein revealed two different genotypes: genotypes I (n = 8) and II (n = 2). Genotype I viruses were most closely related to the NDV V4 strain (n = 7) or the NDV Ulster 2C strain (n = 1). In contrast, genotype II viruses clustered with the NDV vaccine strains (LaSota and VG/GA) that are commonly used as live vaccines in Korea. The epidemiologic importance of NDV at live bird markets in Korea is discussed.
Lee, Myeong-Jin; Miki, Shinichiro; Kitagawa, Masahiro; Lee, Won-Chang
We undertook a comparative analysis of the epidemiology of reported human leptospirosis (HL) cases in Korea and Japan. Between 2006 and 2012, the cumulative incidence of HL in Korea was higher than that in Japan (1.26 vs. 0.14 per 100,000 population, respectively), and the total reported cases were 632 and 196, respectively. Significantly more men were infected than women in both Korea (63.0% men, P < 0.01) and Japan (87.8% men, P < 0.01). In both countries, the incidence was highest among those aged 40 years and older (60%), and peaked in autumn (78.5% cases in Korea, and 46.9% cases in Japan). However, Japan exhibited a significantly higher proportion of male cases, a younger age distribution, and less prominent seasonality. A significant difference was observed in the incidence of HL between the capital city and rural areas in Korea, but not in Japan. The differences in agricultural and forestry practices, and the efficacy or wastewater treatment infrastructure might influence the incidence level in rural areas in both countries. The differences between the 2 countries might be because of their unique geographical characteristics and variations in their levels of industrialization.
Choi, Hye Lim; Suh, Chang-Il; Park, Seung-Won; Jin, Ji-Young; Cho, Han-Gil; Paik, Soon-Young
Sapovirus (SaV), a virus residing in the intestines, is one of the important causes of gastroenteritis in human beings. Human SaV genomes are classified into various genogroups and genotypes. Whole-genome analysis and phylogenetic analysis of ROK62, the SaV isolated in South Korea, were carried out. The ROK62 genome of 7429 nucleotides contains 3 open-reading frames (ORF). The genotype of ROK62 is SaV GI-1, and 94% of its nucleotide sequence is identical with other SaVs, namely Manchester and Mc114. Recently, SaV infection has been on the rise throughout the world, particularly in countries neighboring South Korea; however, very few academic studies have been done nationally. As the first whole-genome sequence analysis of SaV in South Korea, this research will help provide reference for the detection of recombination, tracking of epidemic spread, and development of diagnosis methods for SaV.
FitzGerald, Michael [Broad Institute
Michael FitzGerald on "A rapid whole genome sequencing and analysis system supporting genomic epidemiology" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.
Michael FitzGerald on "A rapid whole genome sequencing and analysis system supporting genomic epidemiology" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.
Jeong, Jae Hoon; Chun, Yeoun Sook; Park, Ki Ho
This study was done to report the epidemiologic characteristics of medical retirement from the Republic of Korea (ROK) Army due to visual impairment and to suggest a practical screening system for the draft. The medical records of 423 eyes of 301 patients who retired from the ROK Army due to visual impairment were reviewed retrospectively between January 2010 and December 2014. The patients were grouped by the presence of trauma, and each group was subdivided by military rank. We analyzed demographic and ophthalmic data, including the etiology of ophthalmologic disease. The etiology was classified into 5 anatomical categories (ocular surface, lens, retina, optic nerve and extraocular visual pathway, and extraocular muscle and orbit), which were then subdivided into the type of disease. The mean age was 24.5 years, and non-traumatic mechanisms accounted for 81.1% (343/423 eyes) of medical retirements. Visual acuity was better in patients without trauma. In enlisted soldiers, disease in the optic nerve and extraocular visual pathway was the most common anatomical category (40.5%), and primary open angle glaucoma (30.8%), retinal dystrophy (18.3%), congenital cataract (14.5%), and retinal detachment (9.7%) were the four most common diseases. Most medical retirements due to visual impairment resulted from non-traumatic mechanisms, even though patients were young. The fundus examination and visual field test would be more useful tools than a conventional vision test for large-scale draft screening for the most common two disease types: primary open angle glaucoma and retinal dystrophy.
Jiao, Jian-Yu; Liu, Lan; Park, Dong-Jin; Kim, Chang-Jin; Xiao, Min; Chen, Jing; Li, Li; Zhong, Jing-Mei; Zhao, Jiao; Li, Wen-Jun
We report the draft genome sequence of Jiangella alkaliphila KCTC 19222(T), isolated from cave soil in Jeju, Republic of Korea. This genome sequence, together with the previously sequenced J. gansuensis strain DSM 44835(T), identified from a desert environmental source, will give us a better understanding of the school of "evolutionary taxonomy."
Jiao, Jian-Yu; Liu, Lan; Park, Dong-Jin; Kim, Chang-Jin; Xiao, Min; Chen, Jing; Li, Li; Zhong, Jing-Mei
We report the draft genome sequence of Jiangella alkaliphila KCTC 19222T, isolated from cave soil in Jeju, Republic of Korea. This genome sequence, together with the previously sequenced J. gansuensis strain DSM 44835T, identified from a desert environmental source, will give us a better understanding of the school of “evolutionary taxonomy.” PMID:26139721
Xu, Yongle; Zheng, Qiang; Liu, Yanting; Jiao, Nianzhi
Salegentibacter salarius KCTC 12974 is isolated from a marine solar saltern of the Yellow Sea in South Korea. Here, we report the draft genome sequence of Salegentibacter salarius KCTC 12974. Various glycoside hydrolase genes in even numbers in the genome reflect the ecological adaption of KCTC 12974 to its habitat. PMID:27881540
Oh, Jae-Young; Kwon, Yong-Kuk; Wei, Bai; Jang, Hyung-Kwan; Lim, Suk-Kyung; Kim, Cheon-Hyeon; Jung, Suk-Chan; Kang, Min-Su
Thirty-nine human isolates of Campylobacter jejuni obtained from a national university hospital during 2007-2010 and 38 chicken isolates of C. jejuni were collected from poultry farms during 2009-2010 in South Korea were used in this study. Campylobacter genomic species and virulence-associated genes were identified by PCR. Pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) were performed to compare their genetic relationships. All isolates were highly resistant to ciprofloxacin, nalidixic acid, and tetracycline. Of all isolates tested, over 94% contained seven virulence associated genes (flaA, cadF, racR, dnaJ, cdtA, cdtB, and cdtC). All isolates were classified into 39 types by PFGE clustering with 90% similarity. Some chicken isolates were incorporated into some PFGE types of human isolates. MLST analysis for the 39 human isolates and 38 chicken isolates resulted in 14 and 23 sequence types (STs), respectively, of which 10 STs were new. STs overlapped in both chicken and human isolates included ST-21, ST-48, ST-50, ST-51, and ST-354, of which ST-21 was the predominant ST in both human and chicken isolates. Through combined analysis of PFGE types and STs, three chicken isolates were clonally related to the three human isolates associated with food poisoning (VII-ST-48, XXII-ST-354, and XXVIII-ST-51). They were derived from geographically same or distinct districts. Remarkably, clonal spread of food poisoning pathogens between animals and humans was confirmed by population genetic analysis. Consequently, contamination of campylobacters with quinolone resistance and potential virulence genes in poultry production and consumption may increase the risk of infections in humans.
Charrel, R N; Coutard, B; Baronti, C; Canard, B; Nougairede, A; Frangeul, A; Morin, B; Jamal, S; Schmidt, C L; Hilgenfeld, R; Klempa, B; de Lamballerie, X
The arenaviruses and hantaviruses are segmented genome RNA viruses that are hosted by rodents. Due to their association with rodents, they are globally widespread and can infect humans via direct or indirect routes of transmission, causing considerable human morbidity and mortality. Nevertheless, despite their obvious and emerging importance as pathogens, there are currently no effective antiviral drugs (except ribavirin which proved effective against Lassa virus) with which to treat humans infected by any of these viruses. The EU-funded VIZIER project (Comparative Structural Genomics of Viral Enzymes Involved in Replication) was instigated with an ultimate view of contributing to the development of antiviral therapies for RNA viruses, including the arenaviruses and bunyaviruses. This review highlights some of the major features of the arenaviruses and hantaviruses that have been investigated during recent years. After describing their classification and epidemiology, we review progress in understanding the genomics as well as the structure and function of replicative enzymes achieved under the VIZIER program and the development of new disease control strategies.
Argimón, Silvia; Abudahab, Khalil; Goater, Richard J. E.; Fedosejev, Artemij; Bhai, Jyothish; Glasner, Corinna; Feil, Edward J.; Holden, Matthew T. G.; Yeats, Corin A.; Grundmann, Hajo; Spratt, Brian G.
Visualization is frequently used to aid our interpretation of complex datasets. Within microbial genomics, visualizing the relationships between multiple genomes as a tree provides a framework onto which associated data (geographical, temporal, phenotypic and epidemiological) are added to generate hypotheses and to explore the dynamics of the system under investigation. Selected static images are then used within publications to highlight the key findings to a wider audience. However, these images are a very inadequate way of exploring and interpreting the richness of the data. There is, therefore, a need for flexible, interactive software that presents the population genomic outputs and associated data in a user-friendly manner for a wide range of end users, from trained bioinformaticians to front-line epidemiologists and health workers. Here, we present Microreact, a web application for the easy visualization of datasets consisting of any combination of trees, geographical, temporal and associated metadata. Data files can be uploaded to Microreact directly via the web browser or by linking to their location (e.g. from Google Drive/Dropbox or via API), and an integrated visualization via trees, maps, timelines and tables provides interactive querying of the data. The visualization can be shared as a permanent web link among collaborators, or embedded within publications to enable readers to explore and download the data. Microreact can act as an end point for any tool or bioinformatic pipeline that ultimately generates a tree, and provides a simple, yet powerful, visualization method that will aid research and discovery and the open sharing of datasets. PMID:28348833
Kim, Jihye; Kwon, Ji-Sun; Kim, Sangsoo
Gene set analysis is a powerful tool for interpreting a genome-wide association study result and is gaining popularity these days. Comparison of the gene sets obtained for a variety of traits measured from a single genetic epidemiology dataset may give insights into the biological mechanisms underlying these traits. Based on the previously published single nucleotide polymorphism (SNP) genotype data on 8,842 individuals enrolled in the Korea Association Resource project, we performed a series of systematic genome-wide association analyses for 49 quantitative traits of basic epidemiological, anthropometric, or blood chemistry parameters. Each analysis result was subjected to subsequent gene set analyses based on Gene Ontology (GO) terms using gene set analysis software, GSA-SNP, identifying a set of GO terms significantly associated to each trait (pcorr < 0.05). Pairwise comparison of the traits in terms of the semantic similarity in their GO sets revealed surprising cases where phenotypically uncorrelated traits showed high similarity in terms of biological pathways. For example, the pH level was related to 7 other traits that showed low phenotypic correlations with it. A literature survey implies that these traits may be regulated partly by common pathways that involve neuronal or nerve systems.
Choi, Jae Bang; Heo, Won Il; Shin, Tae Young; Bae, Sung Min; Kim, Woo Jin; Kim, Ju Il; Kwon, Min; Choi, Jae Young; Je, Yeon Ho; Jin, Byung Rae; Woo, Soo Dong
Mamestra brassicae nucleopolyhedrovirus-K1 (MabrNPV-K1) was isolated from naturally infected M. brassicae (Lepidoptera: Noctuidae) larvae in Korea. The full genome sequences of MabrNPV-K1 were determined, analysed and compared to those of other baculoviruses. The MabrNPV-K1 genome consisted of 152,710 bp and had an overall G + C content of 39.9%. Computer-assisted analysis predicted 158 open reading frames (ORFs) of 150 nucleotides or greater that showed minimal overlap. Two inhibitor of apoptosis (iap) and six baculovirus repeated ORFs were interspersed in the MabrNPV-K1 genome. The unique MabrNPV-K1 ORF133 was identified in the MabrNPV-K1 genome that was not previously reported in baculoviruses. The gene content and arrangement in MabrNPV-K1 had the highest similarity with those of Helicoverpa armigera MNPV (HearMNPV) and Mamestra configurata NPV-B (MacoNPV-B), and their shared homologous genes were 99% collinear. The MabrNPV-K1 genome contained four homologous repeat regions (hr1, hr2, hr3 and hr4) that accounted for 3.3% of the genome. The genomic positions of the four MabrNPV-K1 hr regions were conserved among those of HearMNPV and MacoNPV-B. The gene parity plot, percent identity of the gene homologues and a phylogenetic analysis suggested that these three viruses are closely related not only to each other but also to the same virus strains rather than different virus species.
Lee, Kyu Eun; Park, Young Joo; Cho, Belong; Hwang, Yunji; Choi, June Young; Kim, Su-jin; Choi, Hoonsung; Choi, Ho-Chun; An, Ah Reum; Park, Do Joon; Park, Sue K; Youn, Yeo-Kyu
Introduction Thyroid cancer incidence in Korea is the highest in the world and has recently increased steeply. However, factors contributing to this sudden increase have not been fully elucidated, and few studies have explored the postoperative prognosis. The Thyroid Cancer Longitudinal Study (T-CALOS) was initiated with three aims: (1) to identify factors predicting quality of life, recurrence, and incidence of other diseases after thyroid cancer treatments; (2) to investigate environmental exposure to radiation, toxicants and molecular factors in relation to tumour aggressiveness; and (3) to evaluate gene–environment interactions that increase thyroid cancer in comparison with healthy participants from a pool of nationwide population-based healthy examinees. Methods and analysis T-CALOS enrols patients with incident thyroid cancer from three general hospitals, Seoul National University Hospital, Seoul National University Bundang Hospital and National Medical Center, Korea. The study is an ongoing project expecting to investigate 5000 patients with thyroid cancer up until 2017. Healthy examinees with a normal thyroid confirmed by sonography have been enrolled at the Healthy Examination Center at Seoul National University Hospital. We are also performing individual matching using two nationwide databases that are open to the public. Follow-up information is obtained at patients’ clinical visits and by linkage to the national database. For statistical analysis, we will use conditional logistic regression models and a Cox proportional hazard regression model. A number of stratifications and sensitivity analyses will be performed to confirm the results. Ethics and dissemination Based on a large sample size, a prospective study design, comprehensive data collection and biobank, T-CALOS has been independently peer-reviewed and approved by the three hospitals and two funding sources (National Research Foundation of Korea and Korean Foundation for Cancer Research
Hwang, Jusun; Lee, Kyunglee; Kim, Young-Jun; Sleeman, Jonathan M; Lee, Hang
To assess the status of research on wildlife diseases in the Republic of Korea (ROK) and to identify trends, knowledge gaps, and directions for future research, we reviewed epidemiologic publications on wildlife-associated diseases in the ROK. We identified a relatively small but rapidly increasing body of literature. The majority of publications were focused on public or livestock health and relatively few addressed wildlife health. Most studies that focused on human and livestock health were cross-sectional whereas wildlife health studies were mostly case reports. Fifteen diseases notifiable to the World Organisation for Animal Health were identified and 21 diseases were identified as notifiable to either the Korea Ministry of Health and Welfare or the Korea Ministry of Agriculture, Food and Rural Affairs. Two diseases were reported as occurring as epidemics; highly pathogenic avian influenza (HPAI) and virulent Newcastle disease. Six diseases or disease agents were described in the literature as emerging including HPAI, rabies, Babesia microti , avian coronaviruses, scrub typhus, and severe fever thrombocytopenia syndrome virus. The diseases for which there were the largest number of publications were HPAI and rabies. The majority of wildlife-associated zoonotic disease publications focused on food-borne parasitic infections or rodent-associated diseases. Several publications focused on the potential of wildlife as reservoirs of livestock diseases; in particular, Korean water deer ( Hydropotes inermis argyropus ) and wild boar ( Sus scrofa ). In contrast, there were few publications on diseases of concern for wildlife populations or research to understand the impacts of these diseases for wildlife management. Increased focus on prospective studies would enhance understanding of disease dynamics in wildlife populations. For the high-consequence diseases that impact multiple sectors, a One Health approach, with coordination among the public health, agricultural
Kwon, Nam Hoon; Park, Kun Taek; Jung, Woo Kyung; Youn, Hwa Young; Lee, Yeonhee; Kim, So Hyun; Bae, Wonki; Lim, Ji Youn; Kim, Ji Yeon; Kim, Jun Man; Hong, Soon Keun; Park, Yong Ho
Methicillin resistant Staphylococcus aureus (MRSA) is one of the most important pathogens in human and veterinary hospitals. The isolation of MRSA from animals and foodstuffs has been reported with an increased incidence. However, methicillin (oxacillin) is not used in animal husbandry or in animal hospitals in Korea. In this study, three pre-MRSA and one silent mecA-carrying methicillin susceptible S. aureus (smMSSA) were isolated from retail chicken meat, and three MRSA were isolated from hospitalized dogs in Korea. The three pre-MRSA isolates were determined to have a staphylococcal cassette chromosome mec (SCCmec) type III, and the smMSSA isolate was not classified. The animal hospital isolates were found to contain SCCmec type II. Seven and 15 S. aureus isolated from hospitalized humans and bovine milk, respectively, were also examined in this study in order to determine the epidemiological origins of MRSA. Multilocus sequencing typing (MLST) revealed that the chicken meat and bovine milk isolates were closely related to the animal hospital isolates. The SCCmec characteristics and MLST analyses indicated the possibility of the human to animal transmission of MRSA. These results highlight the importance of identifying MRSA carriers as well as intercepting MRSA transmission because MRSA is becoming increasingly widespread without any plausible relationship with the use of methicillin (oxacillin).
Kuller, Lewis H; Bracken, Michael B; Ogino, Shuji; Prentice, Ross L; Tracy, Russell P
On June 20, 2013, the American Journal of Epidemiology sponsored a symposium at the Society for Epidemiologic Research's 46th Annual Meeting in Boston, Massachusetts, entitled, "What Is the Role of Epidemiology in the Era of Molecular Biology and Genomics?" The future of epidemiology depends on innovation in generating interesting and important testable hypotheses that are relevant to population health. These new strategies will depend on new technology, both in measurement of agents and environment and in the fields of pathophysiology and outcomes, such as cellular epidemiology and molecular pathology. The populations to be studied, sample sizes, and study designs should be selected based on the hypotheses to be tested and include case-control, cohort, and clinical trials. Developing large mega cohorts without attention to specific hypotheses is inefficient, will fail to address many associations with high-quality data, and may well produce spurious results.
Choi, Seung-Kook; Choi, Gug-Seoun; Kwon, Sun-Jung
The complete genome sequences of pepper mild mottle virus (PMMoV)-P2 and -P3 were determined by the Sanger sequencing method. Although PMMoV-P2 and PMMoV-P3 have different pathogenicity in some pepper cultivars, the complete genome sequences of PMMoV-P2 and -P3 are composed of 6,356 nucleotides (nt). In this study, we report the complete genome sequences and genome organization of PMMoV-P2 and -P3 isolates from pepper species in South Korea. PMID:27198033
Moon, Shinje; Han, Jun Hee; Bae, Geun-Ryang; Cho, Enhi; Kim, Bongyoung
The hepatitis A virus (HAV) has been the leading cause of viral hepatitis in Korea since the 2000s. We aimed to describe the current status and regional differences in hepatitis A incidence. We studied the total number of hepatitis A cases reported to the Korea Centers for Disease Control and Prevention through the National Infectious Diseases Surveillance System between 2011 and 2013. Additionally, National Health Insurance Review and Assessment Service data and national population data from Statistics Korea were used. In total, 7,585 hepatitis A cases were reported; 5,521 (10.9 cases per 100,000 populations), 1,197 (2.3 cases per 100,000 populations), and 867 (1.7 cases per 100,000 populations) in 2011, 2012, and 2013, respectively. Fifty-eight patients were infected outside of the country and 7,527 patients represented autochthonous HAV infection cases. Autochthonous HAV infection occurred more frequently among men than women (4,619 cases, 6.1 cases per 100,000 population vs. 2,908 cases, 3.9 cases per 100,000 population). The incidence rate was higher in the 20-29 yr-old group (2,309 cases, 11.6 cases per 100,000 populations) and 30-39 yr-old group (3,306 cases, 13.6 cases per 100,000 populations). The majority of cases were reported from March to June (53.6%, 4,038/7,527). Geographic analyses revealed a consistently high relative risk (RR) of HAV infection in mid-western regions (2011, RR, 1.25, P=0.019; 2012, RR, 2.53, P<0.001; 2013, RR, 1.86, P<0.001). In summary, we report that hepatitis A incidence has been decreasing gradually from 2011 to 2013 and that some regions show the highest prevalence rates of HAV infection in Korea.
Song, Sok; Choe, SeEun; Cha, RaMi; Kim, Ki-Sun; Cho, In-Soo
ABSTRACT The YC16CS (genotype 2.1) strain of classical swine fever virus, isolated from infected pigs in Yeoncheon province, Republic of Korea, near the demilitarized zone, has a high identity with the PC11WB strain of the virus. This is significant in that it is the first case of transmission from wild boars to breed pigs revealed by an epidemiological investigation. PMID:28385854
Wang, An-Hui; Liu, Yuan; Wang, Bo; He, Yi-Xuan; Fang, Ye-Xian; Yan, Yong-Ping
Esophageal cancer (EC) caused about 395000 deaths in 2010. China has the most cases of EC and EC is the fourth leading cause of cancer death in China. Esophageal squamous cell carcinoma (ESCC) is the predominant histologic type (90%-95%), while the incidence of esophageal adenocarcinoma (EAC) remains extremely low in China. Traditional epidemiological studies have revealed that environmental carcinogens are risk factors for EC. Molecular epidemiological studies revealed that susceptibility to EC is influenced by both environmental and genetic risk factors. Of all the risk factors for EC, some are associated with the risk of ESCC and others with the risk of EAC. However, the details and mechanisms of risk factors involved in the process for EC are unclear. The advanced methods and techniques used in human genome studies bring a great opportunity for researchers to explore and identify the details of those risk factors or susceptibility genes involved in the process of EC. Human genome epidemiology is a new branch of epidemiology, which leads the epidemiology study from the molecular epidemiology era to the era of genome wide association studies (GWAS). Here we review the epidemiological studies of EC (especially ESCC) in the era of GWAS, and provide an overview of the general risk factors and those genomic variants (genes, SNPs, miRNAs, proteins) involved in the process of ESCC. PMID:25133033
Risk reasoning has become the common-sense mode of knowledge production in the health sciences. Risk assessment techniques of modern epidemiology also co-shape the ways genomic data are translated into population health. Risk computations (e.g., in preventive medicine, clinical decision-support software, or web-based self-tests), loop results from epidemiological studies back into everyday life. Drawing from observations at various European research sites, I analyze how epidemiological techniques mediate and enact the linkages between genomics and public health. This article examines the epidemiological apparatus as a generative machine that is socially performative. The study design and its reshuffling of data and categories in risk modeling recombine old and new categories from census to genomics and realign genes/environment and nature/culture in novel and hybrid ways. In the Euro-American assemblage of risk reasoning and related profiling techniques, the individual and the population are no longer separate but intimately entangled.
Cha, Se-Yeoun; Kim, Eun-Ju; Kang, Min; Jang, Sang-Ho; Lee, Hae-Beom; Jang, Hyung-Kwan
Raccoon dogs (Nyctereutes procyonoides) are widespread and common in South Korea. In 2011, we obtained serum samples from 102 wild raccoon dogs to survey their exposure to canine distemper virus (CDV). Forty-five of the 102 animals (44.1%) were seropositive. Field cases of canine distemper in wild raccoon dogs from 2010 to 2011 were investigated. Fourteen cases of CDV infection were identified by a commercially available CDV antigen detection kit. These cases were used for virus isolation and molecular analysis. Sequence analysis of hemagglutinin genes indicated that all viruses isolated belonged to the Asia-2 genotype. H protein residues which are related to the receptor and host specificity (residues 530 and 549) were analyzed. A glutamic acid (E) residue is present at 530 in all isolates. At 549, a histidine (H) residue was found in five isolates and tyrosine (Y) residue was found in 6 isolates. Our study demonstrated that CDV infection was widespread in wild raccoon dogs in South Korea.
Lee, Yu Na; Lee, Changhee
A novel cytopathogenic paramyxovirus was isolated from a lung sample from a piglet, using continuous porcine alveolar macrophage cells. Morphologic and genetic studies indicated that this porcine virus (pPIV5) belongs to the species Parainfluenza 5 in the family Paramyxoviridae. We attempted to determine the complete nucleotide sequence of the first Korean pPIV5 isolate, designated KNU-11. The full-length genome of KNU-11 was found to be 15,246 nucleotides in length and consist of seven nonoverlapping genes (3'-N-V/P-M-F-SH-HN-L-5') predicted to encode eight proteins. The overall degree of nucleotide sequence identity was 98.7 % between KNU-11 and PIV5 (formerly simian virus 5, SV5), a prototype paramyxovirus, and the putative proteins had 74.4 to 99.2 % amino acid identity to those of PIV5. Phylogenetic analysis further demonstrated that the novel pPIV5 isolate is a member of the genus Rubulavirus of the subfamily Paramyxovirinae. The present study describes the identification and genomic characterization of a pPIV5 isolate in South Korea.
Gaiarsa, Stefano; De Marco, Leone; Comandatore, Francesco; Marone, Piero; Bandi, Claudio; Sassera, Davide
Bacteriology has embraced the next-generation sequencing revolution, swiftly moving from the time of single genome sequencing to the age of genomic epidemiology. Hundreds and now even thousands of genomes are being sequenced for single bacterial species, allowing unprecedented levels of resolution and insight in the evolution and epidemic diffusion of the main bacterial pathogens. Here, we present a review of some of the most recent and groundbreaking studies in this field. PMID:26878934
Choi, Bong Hwan; Chai, Han Ha; Cho, Yong Min; Jang, Gul Won; Kim, Tae-Hun; Gondro, Cedric; Lee, Seung Hwan
Korean Hanwoo cattle have been subjected to intensive artificial selection over the past four decades to improve meat production traits. Another three cattle varieties very closely related to Hanwoo reside in Korea (Jeju Black and Brindle) and in China (Yanbian). These breeds have not been part of a breeding scheme to improve production traits. Here, we compare the selected Hanwoo against these similar but presumed to be unselected populations to identify genomic regions that have been under recent selection pressure due to the breeding program. Rsb statistics were used to contrast the genomes of Hanwoo versus a pooled sample of the three unselected population (UN). We identified 37 significant SNPs (FDR corrected) in the HW/UN comparison and 21 known protein coding genes were within 1 MB to the identified SNPs. These genes were previously reported to affect traits important for meat production (14 genes), reproduction including mammary gland development (3 genes), coat color (2 genes), and genes affecting behavioral traits in a broader sense (2 genes). We subsequently sequenced (Illumina HiSeq 2000 platform) 10 individuals of the brown Hanwoo and the Chinese Yanbian to identify SNPs within the candidate genomic regions. Based on allele frequency differences, haplotype structures, and literature research, we singled out one non-synonymous SNP in the APP gene (APP: c.569C>T, Ala199Val) and predicted the mutational effect on the protein structure. We found that protein-protein interactions might be impaired due to increased exposed hydrophobic surfaces of the mutated protein. The APP gene has also been reported to affect meat tenderness in pigs and obesity in humans. Meat tenderness has been linked to intramuscular fat content, which is one of the main breeding goals for brown Hanwoo, potentially supporting a causal influence of the herein described nsSNP in the APP gene. PMID:27023061
Méric, Guillaume; Yahara, Koji; Mageiros, Leonardos; Pascoe, Ben; Maiden, Martin C J; Jolley, Keith A; Sheppard, Samuel K
The increasing availability of hundreds of whole bacterial genomes provides opportunities for enhanced understanding of the genes and alleles responsible for clinically important phenotypes and how they evolved. However, it is a significant challenge to develop easy-to-use and scalable methods for characterizing these large and complex data and relating it to disease epidemiology. Existing approaches typically focus on either homologous sequence variation in genes that are shared by all isolates, or non-homologous sequence variation--focusing on genes that are differentially present in the population. Here we present a comparative genomics approach that simultaneously approximates core and accessory genome variation in pathogen populations and apply it to pathogenic species in the genus Campylobacter. A total of 7 published Campylobacter jejuni and Campylobacter coli genomes were selected to represent diversity across these species, and a list of all loci that were present at least once was compiled. After filtering duplicates a 7-isolate reference pan-genome, of 3,933 loci, was defined. A core genome of 1,035 genes was ubiquitous in the sample accounting for 59% of the genes in each isolate (average genome size of 1.68 Mb). The accessory genome contained 2,792 genes. A Campylobacter population sample of 192 genomes was screened for the presence of reference pan-genome loci with gene presence defined as a BLAST match of ≥ 70% identity over ≥ 50% of the locus length--aligned using MUSCLE on a gene-by-gene basis. A total of 21 genes were present only in C. coli and 27 only in C. jejuni, providing information about functional differences associated with species and novel epidemiological markers for population genomic analyses. Homologs of these genes were found in several of the genomes used to define the pan-genome and, therefore, would not have been identified using a single reference strain approach.
Yoon, Young Kyung; Park, Gi Chan; An, Hyonggin; Chun, Byung Chul; Sohn, Jang Wook; Kim, Min Ja
This study determined the trends in the quantities and patterns of nationwide antibiotic consumption in the Republic of Korea (ROK).This nationwide descriptive epidemiological study was conducted in the ROK between 2008 and 2012. The quantities and patterns of total systemic antibiotic prescriptions were analyzed using National Health Insurance claims data collected through the Health Insurance Review and Assessment service. Data concerning systemic antibiotics were collected using measurement units of the defined daily dose (DDD) per 1000 people per day according to the Anatomical Therapeutic Chemical classification.Over the 5-year study period, the annual consumption of systemic antibiotics ranged from 21.68 to 23.12 DDD per 1000 people per day. Outpatient antibiotic use accounted for 80.9% of total consumption. A regression model with autoregressive errors showed significant increased consumption of major antibiotic subgroups, including 3rd-generation cephalosporins, carbapenems, and glycopeptides (P < 0.001). However, the antibiotic use of 1st- (P = 0.003), 2nd- (P = 0.004), and 3rd-generation (P = 0.018) cephalosporins among patients who underwent surgery under monitoring by the antimicrobial stewardship programs for perioperative prescription was significantly lower than in those who underwent surgery without monitoring programs. In time-series analysis, total antibiotic consumption demonstrated significant seasonality (P < 0.001).The consumption of broad-spectrum antibiotics was noted to have increased in the ROK from 2008 to 2012, providing a possible explanation for the changing epidemiology of multidrug resistance. Larger prospective studies are needed to investigate the impact on public health of monitoring programs of perioperative antibiotic usage.
Mackinnon, A; McCallum, J; Andrews, G; Anderson, I
Cultural differences in the reporting of depressive symptoms among older people were examined using the Center for Epidemiological Studies Depression (CES-D) scale in five Southeast Asian countries: Indonesia, Korea, Myanmar, Sri Lanka, and Thailand. Previous work in Asian samples--principally North American immigrants--suggested differential functioning of the CES-D. The four-factor solution established in the original studies of the CES-D was replicated for all countries using a confirmatory factor analytic approach. It was, however, demonstrated that little information was lost in considering full-scale scores rather than the four subscales separately. The behavior of the CES-D in older Asian populations was found to be comparable to results obtained in North American and European cultures. Significant somatization of depression in these Asian samples was not found. There appears to be a general factor measuring depressed mood across older populations. The results support the validity of comparing responses on the CES-D across cultures.
This paper offers a commentary on three aspects of the Supreme Court's recent decision (2011Da22092). First, contrary to the Court's finding, this paper argues that epidemiological evidence can be used to estimate the probability that a given risk factor caused a disease in an individual plaintiff. Second, the distinction between specific and non-specific diseases, upon which the Court relies, is shown to be without scientific basis. Third, this commentary points out that the Court's finding concerning defect of expression effectively enables tobacco companies to profit from the efforts of epidemiologists and others involved in public health to raise awareness of the dangers of smoking.
Shin, Jin-Ho; Sohn, Hyun-Joo; Choi, Kang-Seuk; Kwon, Byung-Jun; Ko, Young-Joon; An, Dong-Jun; Cha, Sang-Ho; Park, Jong-Hyeon; Jeong, Woo-Seog; Park, Jee-Yong; Choi, Cheong-Up; Kweon, Chang-Hee; Song, Jae-Young; Kim, Jong-Yeom; An, Soo-Hwan; Kim, Soon-Jae; Joo, Yi-Seok
The genetic relatedness of 7 Korean type O field strains of foot-and-mouth disease virus (FMDV) in clinical specimens collected from 5 different geographic locations in 2000 was investigated. The sequence of 162 nucleotides (nt 478-639) at the 3' end of the 1D (VP1) genes was determined from amplified cDNA fragments, and subjected to the analysis for the sequence identity/divergence and phylogenetic relationship. The overall nucleotide sequence divergence among the 7 field strains was 0 to 3.8%, suggesting that they are closely related to each other. Phylogenetic analysis with the known Middle East-South Asia (ME-SA) topotype strains showed that the 7 Korean field strains formed two distinct clusters within the same lineage of the ME-SA topotype strains. Cluster 1 consisted of the strains of the primary foci of infection (Paju and Hongseong), and closely related to the strains prevailed in the Far East. Cluster 2 comprised those of subsequently affected regions (Boryeong, Yongin, and Chungju), and was further diverged from the Cluster 1. The result of phylogenetic analysis indicated that the Korean strains may have evolved from a common ancestor of the Pan Asia strains, and that at least 2 phylogenetically clustered variants within the same lineage were prevalent during the epidemic. The potential origin and sources of the virus introduction to Korea were discussed.
Hagymási, Krisztina; Tulassay, Zsolt
The goal of the Human Genome Project to elucidate the complete sequence of the human genome has been achieved. The aims of the "post-genome" era are explaining the genetic information, characterisation of functional elements encoded in the human genome and mapping the human genetic variability as well. Two unrelated human beings also share 99.9% of their genomic sequence. The difference of 0.1% is the result of genetic polymorphisms: single nucleotide polymorphisms, repetitive sequences and insertion/deletion. The genetic differences, coupled with environmental exposures will determine the phenotypic variation we observe in health or disease. The disease-causing genetic variants can be identified by linkage analysis or association studies. The knowledge of human genome and application of multiple biomarkers will improve our ability to identify individuals at risk, so that preventive interventions can be applied, earlier diagnosis can be made and treatment can be optimized.
Yoon, H; Yoon, S-S; Kim, Y-J; Moon, O-K; Wee, S-H; Joo, Y-S; Kim, B
The largest epidemic of foot-and-mouth disease (FMD) in Korea since the first record in 1911 occurred between November 2010 and April 2011. The outbreak was confirmed in 153 farms, and more than three million animals were destroyed. This study presents the temporal and spatial distribution patterns, epidemiological investigation and the control measures for the 2010/2011 epidemic in Korea. The index case of this 2010/2011 FMD epidemic was reported in a pig-farming complex with five piggeries in Andong, GyeongBuk Province, on 28 November 2010, and the outbreak lasted 145 days. The largest number of new detection of the infected farms per day was recorded in mid-January. Epidemiological investigation revealed that the FMD virus had spread from farm to farm through routine movements associated with animal husbandry operations. In contrast to FMD epidemics in other countries in which movement of the infected animals largely contributed to the spread of the disease, human behaviours were major factors in the spread of the FMD virus in the Korean epidemic. The 2010/2011 epidemic was first confirmed in a local small and medium city where share of smallholder producers is higher than that of other provinces. Although Korea had a well-developed emergent response system with the experience of controlling infection and re-obtaining FMD-free status after the previous epidemics, Korea was prompted to revise their contingency plan by tailoring it to its unique livestock environment. Practical contingency plans tailored to Korea for control of FMD can be fully effective when farmers, livestock-related agencies, veterinary service providers and the general public work together.
Lee, Yun-Keun; Ju, Young-Su; Lee, Won Jin; Hwang, Seung Sik; Yim, Sang-Hyuk; Yoo, Sang-Chul; Lee, Jieon; Choi, Kyung-Hwa; Burm, Eunae; Ha, Mina
Objectives We aimed to assess the radiation exposure for epidemiologic investigation in residents exposed to radiation from roads that were accidentally found to be contaminated with radioactive cesium-137 (137Cs) in Seoul. Methods Using information regarding the frequency and duration of passing via the 137Cs contaminated roads or residing/working near the roads from the questionnaires that were obtained from 8875 residents and the measured radiation doses reported by the Nuclear Safety and Security Commission, we calculated the total cumulative dose of radiation exposure for each person. Results Sixty-three percent of the residents who responded to the questionnaire were considered as ever-exposed and 1% of them had a total cumulative dose of more than 10 mSv. The mean (minimum, maximum) duration of radiation exposure was 4.75 years (0.08, 11.98) and the geometric mean (minimum, maximum) of the total cumulative dose was 0.049 mSv (<0.001, 35.35) in the exposed. Conclusions An individual exposure assessment was performed for an epidemiological study to estimate the health risk among residents living in the vicinity of 137Cs contaminated roads. The average exposure dose in the exposed people was less than 5% of the current guideline. PMID:26184047
Byun, Ja Min; Kim, Young Jin; Youk, Taemi; Yang, John Jeongseok; Yoo, Jongha; Park, Tae Sung
Myeloproliferative neoplasms (MPNs), with an expected increment in number, impose substantial economic and social burdens. To this end, we conducted a nationwide population-based descriptive epidemiology study. We also investigated medical cost associated with MPNs. Prevalence was the highest for essential thrombocythemia (ET) (range 4.1-9.0 per 100,000), followed by polycythemia vera (PV) (range 2.8-5.4 per 100,000) and primary myelofibrosis (PMF) (range 0.5-0.9 per 100,000). ET incurred the highest cumulative total cost at US$35 million and the most frequent hospital visits, while PMF incurred the highest average cost per person at US$5000. The mean hemoglobin level was 16.9 ± 2.2 g/dL for PV males and 15.5 ± 2.7 g/dL for PV females. Further analyses on hemoglobin levels showed the true positive rate of PV from the significantly elevated hemoglobin group (defined as >18.5 g/dL for men and >16.5 g/dL for women) was 3.01% and that of MPNs was 3.1%. Here, we provide the biggest population-based report on MPN epidemiology that can readily be used as a representative Asian data.
Reddy, Kondreddy Eswar; Noh, Jin Hyeong; Kim, Young-Ha; Yoo, Mi Sun; Doan, Huong Thi Thanh; Ramya, Mummadireddy; Jung, Suk-Chan; Quyen, Dong Van; Kang, Seung-Won
Phylogenetic trees were constructed for 24 partial nucleotide sequences of the nonstructural polyprotein (ORF1) and structural polyprotein regions (ORF2) of Korean IAPV genotypes, as well as eight previously reported IAPV sequences from various countries. Most of the Korean genotypes formed a distinct cluster, separate from other country genotypes. To investigate this phenomenon in more detail, three complete IAPV genome sequences were identified from different regions in Korea, i.e., Korea1, Korea2, and Korea3. These sequences were aligned with eight previously reported complete genome sequences and various genome regions were compared. The Korean IAPVs were very similar to those from China and Israel, but highly diverged from USA and Australian genotypes. Interestingly, they showed greater variability than the USA and Australian genotypes in ORF1, but highly similar to the Australian genotype in the ORF2 region. Thus, genetic recombination may account for the spatial distance between the Korean IAPV genotypes and those from other countries.
Crawford, Dana C.; Goodloe, Robert; Farber-Eger, Eric; Boston, Jonathan; Pendergrass, Sarah A.; Haines, Jonathan L.; Ritchie, Marylyn D.; Bush, William S.
Background/Aims Present day limited resources demand DNA and phenotyping alternatives to the traditional prospective population-based epidemiologic collections. Methods To accelerate genomic discovery with an emphasis on diverse populations, we as part of the Epidemiologic Architecture for Genes Linked to Environment (EAGLE) study accessed all non-European American samples (n=15,863) available in BioVU, the Vanderbilt University biorepository linked to de-identified electronic medical records, for genomic studies as part of the larger Population Architecture using Genomics and Epidemiology (PAGE) I Study. Given previous studies have cautioned against the secondary use of clinically collected data compared with epidemiologically-collected data, we present here a characterization of EAGLE BioVU, including the billing and diagnostic (ICD-9) code distributions for adult and pediatric patients as well as comparisons made for select health metrics (body mass index, glucose, HbA1c, HDL-C, LDL-C, and triglycerides) with the population-based National Health and Nutrition Examination Surveys (NHANES) linked to DNA samples (NHANES III; n=7,159 and NHANES 1999–2002; n=7,839). Results Overall, the distributions of billing and diagnostic codes suggest this clinical sample is mixture of healthy and sick patients like that expected for a contemporary American population. Conclusion Little bias is observed among health metrics suggesting this clinical collection is suitable for genomic studies along with traditional epidemiologic cohorts. PMID:26201699
This paper offers a commentary on three aspects of the Supreme Court’s recent decision (2011Da22092). First, contrary to the Court’s finding, this paper argues that epidemiological evidence can be used to estimate the probability that a given risk factor caused a disease in an individual plaintiff. Second, the distinction between specific and non-specific diseases, upon which the Court relies, is shown to be without scientific basis. Third, this commentary points out that the Court’s finding concerning defect of expression effectively enables tobacco companies to profit from the efforts of epidemiologists and others involved in public health to raise awareness of the dangers of smoking. PMID:26063352
Hatherell, Hollie-Ann; Didelot, Xavier; Pollock, Sue L.; Tang, Patrick; Crisan, Anamaria; Johnston, James C.; Colijn, Caroline
We report an updated method for inferring the time at which an infectious disease was transmitted between persons from a time-labelled pathogen genome phylogeny. We applied the method to 48 Mycobacterium tuberculosis genomes as part of a real-time public health outbreak investigation, demonstrating that although active tuberculosis (TB) cases were diagnosed through 2013, no transmission events took place beyond mid-2012. Subsequent cases were the result of progression from latent TB infection to active disease, and not recent transmission. This evolutionary genomic approach was used to declare the outbreak over in January 2015. PMID:28348853
Park, Jung Han
Ever since the foundation of the Korean Society for Preventive Medicine in 1947, members of the Society had made remarkable contributions to the public health development and national health promotion. They had played key roles in establishing national health system, improving environmental hygiene, controlling infectious and chronic diseases, promoting family planning, improving industrial and environmental health, and developing health service management. However, the Society had less actively responded to the changes in health service needs of the population that were caused by a rapid epidemiologic transition in last a few decades. Early detection and treatment of chronic diseases including cancer and cardiovascular diseases and risk reduction by the life style modification are major approaches to the contemporary national health problems and they are the core contents of preventive medicine. The author proposed to develop the clinical preventive medicine specialist who will have additional training in clinical medicine for health screening and life style modification to the current preventive medicine training program and thus will be able to provide comprehensive preventive medical services. Another area that the Society may take the initiative is training preventive medicine specialist in the disaster, including bioterrorism, preparedness and management. The Society should be more active in proposing health policy and health service program and also participate collectively in a large scale health research project of the government. These approaches may not only contribute more effectively to the national health promotion but also improve the identity of the Society.
Park, Je-Seop; Cho, Seung-Hak; Youn, Seung-Ki; Bak, Young-Seok; Yu, Young-Bin; Kim, Young Kwon
In order to perform an epidemiological characterization of opportunistic mycosis infections, we collected health insurance data between the years 2006 and 2010 from the Health Insurance Corporation and analyzed the data to determine the prevalence of opportunistic mycoses and treatment management of opportunistic mycoses. The prevalence within the study increased consecutively by 0.02% to 0.12% every year. The annual prevalence of opportunistic mycoses increased from 2.437% in 2006 to 2.709% in 2010. The average annual prevalence was 2.605%. Candidiasis occurred the most frequently, followed by aspergillosis, zygomycosis, and cryptococcosis. The regions with the highest incidences were the capital areas, Gyeonggi and Seoul. By sex, the prevalence in females (4.851%) was 14 times higher than that in males (0.352%). Interestingly, the adults from the 20- to 49-year-old age group showed higher prevalence than children and the elderly. The average duration of hospitalized treatment was 17.31 days and of outpatient treatment was 2.21 days; 3,577 hundred million won was used in total for medical expenses. This study provides useful data to study trends of opportunistic mycoses.
Hwang, Jusun; Lee, Kyunglee; Kim, Young-Jun; Sleeman, Jonathan M.; Lee, Hang
To assess the status of research on wildlife diseases in the Republic of Korea (ROK) and to identify trends, knowledge gaps, and directions for future research, we reviewed epidemiologic publications on wildlife-associated diseases in the ROK. We identified a relatively small but rapidly increasing body of literature. The majority of publications were focused on public or livestock health and relatively few addressed wildlife health. Most studies that focused on human and livestock health were cross-sectional whereas wildlife health studies were mostly case reports. Fifteen diseases notifiable to the World Organisation for Animal Health were identified and 21 diseases were identified as notifiable to either the Korean Ministry of Health, Welfare, and Family Affairs or the Korean Ministry of Agriculture. Two diseases were reported as occurring as epidemics; highly pathogenic avian influenza (HPAI) and virulent Newcastle disease. Six diseases or disease agents were described in the literature as emerging including HPAI, rabies, Babesia microti, avian coronaviruses, scrub typhus, and severe fever thrombocytopenia syndrome virus. The diseases for which there were the largest number of publications were HPAI and rabies. The majority of wildlife-associated zoonotic disease publications focused on food-borne parasitic infections or rodent-associated diseases. Several publications focused on the potential of wildlife as reservoirs of livestock diseases; in particular, water deer (Hydropotes inermis) and wild boar (Sus scrofa). In contrast, there were few publications on diseases of concern for wildlife populations or research to understand the impacts of these diseases for wildlife management. Increased focus on prospective studies would enhance understanding of disease dynamics in wildlife populations. For the high-consequence diseases that impact multiple sectors, a One Health approach, with coordination among the public health, agricultural, and environmental sectors
Kim, Semi; Sung, Ji Youn; Cho, Hye Hyun; Kwon, Kye Chul; Koo, Sun Hoe
The aims of this study were to characterize the molecular epidemiological profiles of CTX-M-producing uropathogenic Escherichia coli isolates from a tertiary hospital in Daejeon, Korea, and to investigate the genetic diversity and compare the prevalence of sequence types (STs) in different areas. Extended spectrum β-lactamase-producing E. coli strains isolated from urine were analyzed for CTX-M, integrons, and insertion sequence common regions (ISCRs) by PCR and sequencing. Multilocus sequence typing (MLST), pulsed-field gel electrophoresis (PFGE), phylogenetic analysis, and rep-PCR were also used for molecular typing of the isolates. Of 80 CTX-M producers, 31 and 46 expressed CTX-M-15 and CTX-M-14, respectively. MLST analysis indicated that the most prevalent ST was ST131 (n = 34, 42.5%), followed by ST38 (n = 22, 27.5%), ST405 (n = 8, 10.0%), and ST69 (n = 6, 7.5%). Most CTX-M producers harbored class 1 integrons. ST131 strains belonged to phylogenetic group B2 and showed identical rep-PCR patterns, whereas ST69, ST38, and ST405 strains belonged to phylogenetic group D; the ST38 and ST405 strains displayed the same rep-PCR pattern, respectively. ST131 and ST38 isolates showed 21 and 19 distinct types, respectively, by PFGE. In Daejeon, D-ST38 CTX-M-14 producers were relatively more prevalent than in other countries and Korean cities. Our results indicate that CTX-M-producing E. coli isolates belonged mostly to ST131 or ST38 and were more related to hospital-onset than to community-onset infections and that the blaCTX-M gene may vary according to the ST.
Kim, Changsoo; Shin, Dong Chun; Yong, Tai Soon; Oh, Dae Kyu; Kim, Rock Kwon; Park, Keeho; Suh, I. L.
OBJECTIVE: In the Republic of Korea (ROK), soldiers stationed where there is a risk of contracting malaria have received antimalarial chemoprophylaxis since 1997. However, chemoprophylaxis may facilitate the development of drug resistance, and late primary attacks in individuals who have received chemoprophylaxis are becoming more frequent. We investigated the association between chemoprophylaxis and the epidemiological characteristics and effectiveness of treatment for re-emergent Plasmodium vivax malaria, using a nationwide malaria database. METHODS: Among soldiers at risk of malaria between 1999 and 2001, we reviewed all P. vivax malaria cases (1158) that occurred before 31 December 2003. Early and late primary attacks were defined as cases occurring
Willems, Stefanie; Kampmeier, Stefanie; Bletz, Stefan; Kossow, Annelene; Köck, Robin; Kipp, Frank
We characterized two epidemiologically similar Acinetobacter baumannii clusters from two separate intensive care units (ICU) using core genome multilocus sequence typing. Clonal spread was confirmed in ICU-1 (12 of 14 isolates shared genotypes); in ICU-2, all genotypes (13 isolates) were diverse, thus excluding transmissions and enabling adequate infection control measures. PMID:27358465
Cho, Ja Young; Cho, Dae-Yeon; Ahn, Sei Hyun; Choi, Su-Youn; Shin, Inkyung; Park, Hyun Gyu; Lee, Jong Won; Kim, Hee Jeong; Yu, Jong Han; Ko, Beom Seok; Ku, Bo Kyung; Son, Byung Ho
We screened large genomic rearrangements of the BRCA1 and BRCA2 genes in Korean, familial breast cancer patients. Multiplex ligation-dependent probe amplification assay was used to identify BRCA1 and BRCA2 genomic rearrangements in 226 Korean familial breast cancer patients with risk factors for BRCA1 and BRCA2 mutations, who previously tested negative for point mutations in the two genes. We identified only one large deletion (c.4186-1593_4676-1465del) in BRCA1. No large rearrangements were found in BRCA2. Our result indicates that large genomic rearrangement in the BRCA1 and BRCA2 genes does not seem like a major determinant of breast cancer susceptibility in the Korean population. A large-scale study needs to validate our result in Korea.
Savage, Sharon A.; Mirabello, Lisa
Osteosarcoma is a primary bone malignancy that typically occurs during adolescence but also has a second incidence peak in the elderly. It occurs most commonly in the long bones, although there is variability in location between age groups. The etiology of osteosarcoma is not well understood; it occurs at increased rates in individuals with Paget disease of bone, after therapeutic radiation, and in certain cancer predisposition syndromes. It also occurs more commonly in taller individuals, but a strong environmental component to osteosarcoma risk has not been identified. Several studies suggest that osteosarcoma may be associated with single nucleotide polymorphisms in genes important in growth and tumor suppression but the studies are limited by sample size. Herein, we review the epidemiology of osteosarcoma as well as its known and suspected risk factors in an effort to gain insight into its etiology. PMID:21437228
Reddy, Kondreddy Eswar; Yoo, Mi Sun; Kim, Young-Ha; Kim, Nam-Hee; Ramya, Mummadireddy; Jung, Ha-Na; Thao, Le Thi Bich; Lee, Hee-Soo; Kang, Seung-Won
Sacbrood virus (SBV) represents a serious threat to the health of managed honeybees. We determined four complete SBV genomic sequences (AmSBV-Kor1, AmSBV-Kor2, AcSBV-Kor3, and AcSBV-Kor4) isolated from Apis mellifera and Apis cerana in various regions of South Korea. A phylogenetic tree was constructed from the complete genomic sequences of these Korean SBVs (KSBVs) and 21 previously reported SBV sequences from other countries. Three KSBVs (not AmSBV-Kor1) clustered with previously reported Korean genomes, but separately from SBV genomes from other countries. The KSBVs shared 90-98 % identity, and 89-97 % identity with the genomes from other countries. AmSBV-Kor1 was least similar (~90 % identity) to the other KSBVs, and was most similar to previously reported strains AmSBV-Kor21 (97 %) and AmSBV-UK (93 %). Phylogenetic analysis of the partial VP1 region sequences indicated that SBVs clustered by host species and country of origin. The KSBVs were aligned with nine previously reported complete SBV genomes and compared. The KSBVs were most different from the other genomes at the end of the 5' untranslated region and in the entire open reading frame. A SimPlot graph of the VP1 region confirmed its high variability, especially between the SBVs infecting A. mellifera and A. cerana. In this genomic region, SBVs from A. mellifera species contain an extra continuous 51-nucleotide sequence relative to the SBVs from A. cerana. This genomic diversity may reflect the adaptation of SBV to specific hosts, viral cross-infections, and the spatial distances separating the KSBVs from other SBVs.
Mustapha, Mustapha M.; Marsh, Jane W.; Krauland, Mary G.; Fernandez, Jorge O.; de Lemos, Ana Paula S.; Dunning Hotopp, Julie C.; Wang, Xin; Mayer, Leonard W.; Lawrence, Jeffrey G.; Hiller, N. Luisa; Harrison, Lee H.
Neisseria meningitidis is a leading bacterial cause of sepsis and meningitis globally with dynamic strain distribution over time. Beginning with an epidemic among Hajj pilgrims in 2000, serogroup W (W) sequence type (ST) 11 emerged as a leading cause of epidemic meningitis in the African ‘meningitis belt’ and endemic cases in South America, Europe, Middle East and China. Previous genotyping studies were unable to reliably discriminate sporadic W ST-11 strains in circulation since 1970 from the Hajj outbreak strain (Hajj clone). It is also unclear what proportion of more recent W ST-11 disease clusters are caused by direct descendants of the Hajj clone. Whole genome sequences of 270 meningococcal strains isolated from patients with invasive meningococcal disease globally from 1970 to 2013 were compared using whole genome phylogenetic and major antigen-encoding gene sequence analyses. We found that all W ST-11 strains were descendants of an ancestral strain that had undergone unique capsular switching events. The Hajj clone and its descendants were distinct from other W ST-11 strains in that they shared a common antigen gene profile and had undergone recombination involving virulence genes encoding factor H binding protein, nitric oxide reductase, and nitrite reductase. These data demonstrate that recent acquisition of a distinct antigen-encoding gene profile and variations in meningococcal virulence genes was associated with the emergence of the Hajj clone. Importantly, W ST-11 strains unrelated to the Hajj outbreak contribute a significant proportion of W ST-11 cases globally. This study helps illuminate genomic factors associated with meningococcal strain emergence and evolution. PMID:26629539
Lee, Wan-Ji; Jung, Hee-Dong; Cheong, Hyang-Min; Kim, Kisoon
An outbreak of upper respiratory tract infections associated with human adenovirus (HAdV) occurred on a national scale in Korea from September to December 2010, following a major H1N1 influenza pandemic. Data from the Korea Influenza and Respiratory Surveillance System (KINRESS) showed an unusually high positive rate accounting for up to 20% of all diagnosed cases. To determine the principal cause of the outbreak, direct polymerase chain reaction (PCR) amplification followed by sequence analysis targeting parts of the hexon gene of HAdV was performed. Serotypes of 1,007 PCR-diagnosed HAdV-positive samples from patients with an acute upper respiratory tract illness were determined and epidemiological characteristics including major aged group and clinical symptoms were analyzed. The principal symptom of HAdV infections was fever and the vulnerable aged group was 1-5 years old. Based on sequence analysis, HAdV-3 was the predominant serotype in the outbreak, with an incidence of 74.3%. From the beginning of 2010 until May, the major serotypes were HAdV-1, 2, and 5 (70-100%) in any given period. However, an outbreak dominated by HAdV-3 started between July and August and peaked in September. Phylogenetic analysis revealed that there was no genetic variation in HAdV-3. The results demonstrated that an outbreak of upper respiratory illness followed by H1N1 influenza pandemic in Korea was caused mainly by emerged HAdV-3. J.
Shafi, Jamila; Andrew, Peter W.
In response to a large local school-based outbreak of tuberculosis, we have been evaluating the utility of microarray bacterial genomic analysis in outbreak management. After initial comparison of the isolate from the index case with Mycobacterium tuberculosis H37Rv, it was possible to design robust PCRs directed towards strain-specific deletions. Rapid PCR analysis of isolates proved valuable in determining whether or not other isolates were compatible with the outbreak strain and further microarray studies revealed genetic markers that could be used to discriminate between locally circulating strains.We suggest that this approach forms the basis for developing rapid local genotyping schemes applicable to M. tuberculosis and that application to other pathogens warrants consideration. PMID:18629269
Croucher, Nicholas J.; Finkelstein, Jonathan A.; Pelton, Stephen I.; Parkhill, Julian; Bentley, Stephen D.; Lipsitch, Marc; Hanage, William P.
Streptococcus pneumoniae is common nasopharyngeal commensal bacterium and important human pathogen. Vaccines against a subset of pneumococcal antigenic diversity have reduced rates of disease, without changing the frequency of asymptomatic carriage, through altering the bacterial population structure. These changes can be studied in detail through using genome sequencing to characterise systematically-sampled collections of carried S. pneumoniae. This dataset consists of 616 annotated draft genomes of isolates collected from children during routine visits to primary care physicians in Massachusetts between 2001, shortly after the seven valent polysaccharide conjugate vaccine was introduced, and 2007. Also made available are a core genome alignment and phylogeny describing the overall population structure, clusters of orthologous protein sequences, software for inferring serotype from Illumina reads, and whole genome alignments for the analysis of closely-related sets of pneumococci. These data can be used to study both bacterial evolution and the epidemiology of a pathogen population under selection from vaccine-induced immunity. PMID:26528397
Hill, Sarah C; Lee, Youn-Jeong; Song, Byung-Min; Kang, Hyun-Mi; Lee, Eun-Kyoung; Hanna, Amanda; Gilbert, Marius; Brown, Ian H; Pybus, Oliver G
Highly pathogenic avian influenza (HPAI) viruses threaten human and animal health yet their emergence is poorly understood, partly because sampling of the HPAI Asian-origin H5N1 lineage immediately after its identification in 1996 was comparatively sparse. The discovery of a novel H5N8 virus in 2013 provides a new opportunity to investigate HPAI emergence in greater detail. Here we investigate the origin and transmission of H5N8 in the Republic of Korea, the second country to report the new strain. We reconstruct viral spread using phylogeographic methods and interpret the results in the context of ecological data on poultry density, overwintering wild bird numbers, and bird migration patterns. Our results indicate that wild waterfowl migration and domestic duck density were important to H5N8 epidemiology. Specifically, we infer that H5N8 entered the Republic of Korea via Jeonbuk province, then spread rapidly among western provinces where densities of overwintering waterfowl and domestic ducks are higher, yet rarely persisted in eastern regions. The common ancestor of H5N8 in the Republic of Korea was estimated to have arrived during the peak of inward migration of overwintering birds. Recent virus isolations likely represent re-introductions via bird migration from an as-yet unsampled reservoir. Based on the limited data from outside the Republic of Korea, our data suggest that H5N8 may have entered Europe at least twice, and Asia at least three times from this reservoir, most likely carried by wild migrating birds.
Hill, Sarah C.; Lee, Youn-Jeong; Song, Byung-Min; Kang, Hyun-Mi; Lee, Eun-Kyoung; Hanna, Amanda; Gilbert, Marius; Brown, Ian H.; Pybus, Oliver G.
Highly pathogenic avian influenza (HPAI) viruses threaten human and animal health yet their emergence is poorly understood, partly because sampling of the HPAI Asian-origin H5N1 lineage immediately after its identification in 1996 was comparatively sparse. The discovery of a novel H5N8 virus in 2013 provides a new opportunity to investigate HPAI emergence in greater detail. Here we investigate the origin and transmission of H5N8 in the Republic of Korea, the second country to report the new strain. We reconstruct viral spread using phylogeographic methods and interpret the results in the context of ecological data on poultry density, overwintering wild bird numbers, and bird migration patterns. Our results indicate that wild waterfowl migration and domestic duck density were important to H5N8 epidemiology. Specifically, we infer that H5N8 entered the Republic of Korea via Jeonbuk province, then spread rapidly among western provinces where densities of overwintering waterfowl and domestic ducks are higher, yet rarely persisted in eastern regions. The common ancestor of H5N8 in the Republic of Korea was estimated to have arrived during the peak of inward migration of overwintering birds. Recent virus isolations likely represent re-introductions via bird migration from an as-yet unsampled reservoir. Based on the limited data from outside the Republic of Korea, our data suggest that H5N8 may have entered Europe at least twice, and Asia at least three times from this reservoir, most likely carried by wild migrating birds. PMID:26079277
Leekitcharoenphon, Pimlapas; Hendriksen, Rene S.; Le Hello, Simon; ...
It has been 30 years since the initial emergence and subsequent rapid global spread of multidrug-resistant Salmonella enterica serovar Typhimurium DT104 (MDR DT104). Nonetheless, its origin and transmission route have never been revealed. In this paper, we used whole-genome sequencing (WGS) and temporally structured sequence analysis within a Bayesian framework to reconstruct temporal and spatial phylogenetic trees and estimate the rates of mutation and divergence times of 315 S. Typhimurium DT104 isolates sampled from 1969 to 2012 from 21 countries on six continents. DT104 was estimated to have emerged initially as antimicrobial susceptible in ~1948 (95% credible interval [CI], 1934more » to 1962) and later became MDR DT104 in ~1972 (95% CI, 1972 to 1988) through horizontal transfer of the 13-kb Salmonella genomic island 1 (SGI1) MDR region into susceptible strains already containing SGI1. This was followed by multiple transmission events, initially from central Europe and later between several European countries. An independent transmission to the United States and another to Japan occurred, and from there MDR DT104 was probably transmitted to Taiwan and Canada. An independent acquisition of resistance genes took place in Thailand in ~1975 (95% CI, 1975 to 1990). In Denmark, WGS analysis provided evidence for transmission of the organism between herds of animals. Interestingly, the demographic history of Danish MDR DT104 provided evidence for the success of the program to eradicate Salmonella from pig herds in Denmark from 1996 to 2000. Finally, the results from this study refute several hypotheses on the evolution of DT104 and suggest that WGS may be useful in monitoring emerging clones and devising strategies for prevention of Salmonella infections.« less
Leekitcharoenphon, Pimlapas; Hendriksen, Rene S.; Le Hello, Simon; Weill, François-Xavier; Baggesen, Dorte Lau; Jun, Se-Ran; Ussery, David W.; Lund, Ole; Crook, Derrick W.; Wilson, Daniel J.; Aarestrup, Frank M.
It has been 30 years since the initial emergence and subsequent rapid global spread of multidrug-resistant Salmonella enterica serovar Typhimurium DT104 (MDR DT104). Nonetheless, its origin and transmission route have never been revealed. In this paper, we used whole-genome sequencing (WGS) and temporally structured sequence analysis within a Bayesian framework to reconstruct temporal and spatial phylogenetic trees and estimate the rates of mutation and divergence times of 315 S. Typhimurium DT104 isolates sampled from 1969 to 2012 from 21 countries on six continents. DT104 was estimated to have emerged initially as antimicrobial susceptible in ~1948 (95% credible interval [CI], 1934 to 1962) and later became MDR DT104 in ~1972 (95% CI, 1972 to 1988) through horizontal transfer of the 13-kb Salmonella genomic island 1 (SGI1) MDR region into susceptible strains already containing SGI1. This was followed by multiple transmission events, initially from central Europe and later between several European countries. An independent transmission to the United States and another to Japan occurred, and from there MDR DT104 was probably transmitted to Taiwan and Canada. An independent acquisition of resistance genes took place in Thailand in ~1975 (95% CI, 1975 to 1990). In Denmark, WGS analysis provided evidence for transmission of the organism between herds of animals. Interestingly, the demographic history of Danish MDR DT104 provided evidence for the success of the program to eradicate Salmonella from pig herds in Denmark from 1996 to 2000. Finally, the results from this study refute several hypotheses on the evolution of DT104 and suggest that WGS may be useful in monitoring emerging clones and devising strategies for prevention of Salmonella infections.
Leekitcharoenphon, Pimlapas; Hendriksen, Rene S; Le Hello, Simon; Weill, François-Xavier; Baggesen, Dorte Lau; Jun, Se-Ran; Ussery, David W; Lund, Ole; Crook, Derrick W; Wilson, Daniel J; Aarestrup, Frank M
It has been 30 years since the initial emergence and subsequent rapid global spread of multidrug-resistant Salmonella entericaserovar Typhimurium DT104 (MDR DT104). Nonetheless, its origin and transmission route have never been revealed. We used whole-genome sequencing (WGS) and temporally structured sequence analysis within a Bayesian framework to reconstruct temporal and spatial phylogenetic trees and estimate the rates of mutation and divergence times of 315S Typhimurium DT104 isolates sampled from 1969 to 2012 from 21 countries on six continents. DT104 was estimated to have emerged initially as antimicrobial susceptible in ∼1948 (95% credible interval [CI], 1934 to 1962) and later became MDR DT104 in ∼1972 (95% CI, 1972 to 1988) through horizontal transfer of the 13-kb Salmonella genomic island 1 (SGI1) MDR region into susceptible strains already containing SGI1. This was followed by multiple transmission events, initially from central Europe and later between several European countries. An independent transmission to the United States and another to Japan occurred, and from there MDR DT104 was probably transmitted to Taiwan and Canada. An independent acquisition of resistance genes took place in Thailand in ∼1975 (95% CI, 1975 to 1990). In Denmark, WGS analysis provided evidence for transmission of the organism between herds of animals. Interestingly, the demographic history of Danish MDR DT104 provided evidence for the success of the program to eradicate Salmonellafrom pig herds in Denmark from 1996 to 2000. The results from this study refute several hypotheses on the evolution of DT104 and suggest that WGS may be useful in monitoring emerging clones and devising strategies for prevention of Salmonella infections.
Hendriksen, Rene S.; Le Hello, Simon; Weill, François-Xavier; Baggesen, Dorte Lau; Jun, Se-Ran; Lund, Ole; Crook, Derrick W.; Wilson, Daniel J.; Aarestrup, Frank M.
It has been 30 years since the initial emergence and subsequent rapid global spread of multidrug-resistant Salmonella enterica serovar Typhimurium DT104 (MDR DT104). Nonetheless, its origin and transmission route have never been revealed. We used whole-genome sequencing (WGS) and temporally structured sequence analysis within a Bayesian framework to reconstruct temporal and spatial phylogenetic trees and estimate the rates of mutation and divergence times of 315 S. Typhimurium DT104 isolates sampled from 1969 to 2012 from 21 countries on six continents. DT104 was estimated to have emerged initially as antimicrobial susceptible in ∼1948 (95% credible interval [CI], 1934 to 1962) and later became MDR DT104 in ∼1972 (95% CI, 1972 to 1988) through horizontal transfer of the 13-kb Salmonella genomic island 1 (SGI1) MDR region into susceptible strains already containing SGI1. This was followed by multiple transmission events, initially from central Europe and later between several European countries. An independent transmission to the United States and another to Japan occurred, and from there MDR DT104 was probably transmitted to Taiwan and Canada. An independent acquisition of resistance genes took place in Thailand in ∼1975 (95% CI, 1975 to 1990). In Denmark, WGS analysis provided evidence for transmission of the organism between herds of animals. Interestingly, the demographic history of Danish MDR DT104 provided evidence for the success of the program to eradicate Salmonella from pig herds in Denmark from 1996 to 2000. The results from this study refute several hypotheses on the evolution of DT104 and suggest that WGS may be useful in monitoring emerging clones and devising strategies for prevention of Salmonella infections. PMID:26944846
Oetjens, Matthew T.; Brown-Gentry, Kristin; Goodloe, Robert; Dilks, Holli H.; Crawford, Dana C.
Population stratification or confounding by genetic ancestry is a potential cause of false associations in genetic association studies. Estimation of and adjustment for genetic ancestry has become common practice thanks in part to the availability of ancestry informative markers on genome-wide association study (GWAS) arrays. While array data is now widespread, these data are not ubiquitous as several large epidemiologic and clinic-based studies lack genome-wide data. One such large epidemiologic-based study lacking genome-wide data accessible to investigators is the National Health and Nutrition Examination Surveys (NHANES), population-based cross-sectional surveys of Americans linked to demographic, health, and lifestyle data conducted by the Centers for Disease Control and Prevention. DNA samples (n = 14,998) were extracted from biospecimens from consented NHANES participants between 1991–1994 (NHANES III, phase 2) and 1999–2002 and represent three major self-identified racial/ethnic groups: non-Hispanic whites (n = 6,634), non-Hispanic blacks (n = 3,458), and Mexican Americans (n = 3,950). We as the Epidemiologic Architecture for Genes Linked to Environment study genotyped candidate gene and GWAS-identified index variants in NHANES as part of the larger Population Architecture using Genomics and Epidemiology I study for collaborative genetic association studies. To enable basic quality control such as estimation of genetic ancestry to control for population stratification in NHANES san genome-wide data, we outline here strategies that use limited genetic data to identify the markers optimal for characterizing genetic ancestry. From among 411 and 295 autosomal SNPs available in NHANES III and NHANES 1999–2002, we demonstrate that markers with ancestry information can be identified to estimate global ancestry. Despite limited resolution, global genetic ancestry is highly correlated with self-identified race for the majority of participants, although less so
Oem, Jae-Ku; Kim, Seong-Hee; Kim, Yeon-Hee; Lee, Myoung-Heon; Lee, Kyoung-Ki
The complete genomes of three rabies viruses (BD0406CC, BV9901PJ, and 08F40) of two raccoon dogs (Nyctereutes procyonoides koreensis) and a cow were determined. The genomic organization is typical of rabies viruses, and the open reading frames of the N, P, M, G, and L genes are 1,353, 894, 609, 1,575, and 6,384 bases in length, respectively. The full genome length of the three strains was 11,928 nucleotides, and the sequence similarity between the rabies viruses at the nucleotide level was 98.5-99.5%. Sequence comparisons indicated that these rabies viruses belong to the "Arctic and Arctic-like" group, with high homology to the Eurasian cluster. All Korean strains were clustered with the Mongolia strains, which belong to Arctic-like 1 clade. The 08F40 and BD0406CC strains were constructed with rabies virus strains isolated in Gangwon province. The BV9901PJ strain was closely related to strains isolated in Gyeonggi province in Korea. Three strains were more dependent upon geographical distribution and time period than host species. Complete genome sequencing of different host-origin rabies viruses will provide information that should contribute to understanding the transmission cycle and genetic variability of rabies from different hosts.
Visnovsky, Sandra B; Panda, Preetinanda; Taylor, Robert; Pitman, Andrew R
Pectobacterium carotovorum subsp. actinidiae is the causal agent of summer canker in kiwifruit plants in South Korea. We report here the draft genome sequences of two P. carotovorum subsp. actinidiae strains, ICMP 19971 and ICMP 19972, which were originally isolated from Actinidia chinensis with symptoms of summer canker. These genome sequences will aid in the identification of genetic traits associated with their unusual capacity to cause canker and help understanding of the threat these exotic enterobacteria pose to the New Zealand kiwifruit industry.
Joo, So-Young; Goo, Youn-Kyoung; Ryu, Jae-Sook; Lee, Sang-Eun; Lee, Won Kee; Chung, Dong-Il; Hong, Yeonchul
Trichomoniasis, which is caused by Trichomonas vaginalis, is one of the most common non-viral sexually transmitted infections; however, limited population-based data are available that describe patterns and trends of the disease. We summarized insurance claims of trichomoniasis cases reported during 2009–2014 to South Korea Health Insurance Review and Assessment Service. The average annual incidence in South Korea was 276.8 persons per 100,000 population, and a substantial sex-associated variation was observed. The incidence rate among female subjects trended upward over 6 years, that is, it increased from 501 in 2009 to 625.8 in 2014 per 100,000 female population, which indicates a 25% overall increase. This trend was sharpest in the ≥60 years group of female population. However, a 66% decrease in incidence rates was observed among male subjects (23.7 in 2009 to 15.7 in 2014 per 100,000 male population). Further, substantial decrease was observed in the ≥40 years groups of male population. The incidence of trichomoniasis varied across regions and was the highest in Jeju province of South Korea. Overall, as the incidence of trichomoniasis appears to have increased in South Korea during 2009–2014, the disease burden is increasing; hence, there is a need to better understand the disease transmission. PMID:27936227
Breurec, Sebastien; Criscuolo, Alexis; Diancourt, Laure; Rendueles, Olaya; Vandenbogaert, Mathias; Passet, Virginie; Caro, Valérie; Rocha, Eduardo P C; Touchon, Marie; Brisse, Sylvain
Elizabethkingia anophelis is an emerging pathogen involved in human infections and outbreaks in distinct world regions. We investigated the phylogenetic relationships and pathogenesis-associated genomic features of two neonatal meningitis isolates isolated 5 years apart from one hospital in Central African Republic and compared them with Elizabethkingia from other regions and sources. Average nucleotide identity firmly confirmed that E. anophelis, E. meningoseptica and E. miricola represent demarcated genomic species. A core genome multilocus sequence typing scheme, broadly applicable to Elizabethkingia species, was developed and made publicly available (http://bigsdb.pasteur.fr/elizabethkingia). Phylogenetic analysis revealed distinct E. anophelis sublineages and demonstrated high genetic relatedness between the African isolates, compatible with persistence of the strain in the hospital environment. CRISPR spacer variation between the African isolates was mirrored by the presence of a large mobile genetic element. The pan-genome of E. anophelis comprised 6,880 gene families, underlining genomic heterogeneity of this species. African isolates carried unique resistance genes acquired by horizontal transfer. We demonstrated the presence of extensive variation of the capsular polysaccharide synthesis gene cluster in E. anophelis. Our results demonstrate the dynamic evolution of this emerging pathogen and the power of genomic approaches for Elizabethkingia identification, population biology and epidemiology.
Breurec, Sebastien; Criscuolo, Alexis; Diancourt, Laure; Rendueles, Olaya; Vandenbogaert, Mathias; Passet, Virginie; Caro, Valérie; Rocha, Eduardo P. C.; Touchon, Marie; Brisse, Sylvain
Elizabethkingia anophelis is an emerging pathogen involved in human infections and outbreaks in distinct world regions. We investigated the phylogenetic relationships and pathogenesis-associated genomic features of two neonatal meningitis isolates isolated 5 years apart from one hospital in Central African Republic and compared them with Elizabethkingia from other regions and sources. Average nucleotide identity firmly confirmed that E. anophelis, E. meningoseptica and E. miricola represent demarcated genomic species. A core genome multilocus sequence typing scheme, broadly applicable to Elizabethkingia species, was developed and made publicly available (http://bigsdb.pasteur.fr/elizabethkingia). Phylogenetic analysis revealed distinct E. anophelis sublineages and demonstrated high genetic relatedness between the African isolates, compatible with persistence of the strain in the hospital environment. CRISPR spacer variation between the African isolates was mirrored by the presence of a large mobile genetic element. The pan-genome of E. anophelis comprised 6,880 gene families, underlining genomic heterogeneity of this species. African isolates carried unique resistance genes acquired by horizontal transfer. We demonstrated the presence of extensive variation of the capsular polysaccharide synthesis gene cluster in E. anophelis. Our results demonstrate the dynamic evolution of this emerging pathogen and the power of genomic approaches for Elizabethkingia identification, population biology and epidemiology. PMID:27461509
Kim, A Reum; Chung, Hee Chun; Kim, Hye Kwon; Kim, Eun Ok; Nguyen, Van Giap; Choi, Min Gyung; Yang, Hye Jung; Kim, Jung Ah; Park, Bong Kyun
Porcine circular single-stranded DNA viruses have been just identified from swine feces in Korea. This virus was mentioned as bovine stool-associated circular DNA virus (BoSCV)-like virus discovered from porcine stools. However, the thorough characteristics of the virus were not identified. Therefore, this research focuses on finding a full genome sequence and analyzing the genetic features of the virus. The virus, now called porcine stool-associated circular DNA virus in Korea (PoSCV Kor), consists of 2,589 bases forming circular structure. It has two major ORFs inversely encoding replicase and capsid protein, with each stem-loop structure between 5' ends and 3' ends of the two putative ORFs. This characteristics is the same as PoSCV in New Zealand, but different from chimpanzee stool-associated circular virus (ChiSCVs) and BoSCV, which have one stem-loop structure. Therefore, it would be sure that PoSCV Kor is very similar to PoSCV in respect to the genetic aspect; the same number of nucleotide bases and the amino acid identity of replicase and capsid protein (96 and 93 %, respectively). This fact could be certified through the finding that PoSCV Kor and PoSCV are in the same cluster by phylogenetic analysis based on the comparison with full-sequences of other circular ssDNA viruses.
Ha, Hyun-Ju; Lee, Sung-Geun; Cho, Han-Gil; Jin, Ji-Young; Lee, Jae Woong; Paik, Soon-Yong
Human astroviruses (HAstVs) occur worldwide and are known to the causative agents of diarrhea in infants and elderly patients with immune dysfunction. This study aimed to identify recombinant HAstV strains and characterize rare genotypes. The full-length genome of a recombinant HAstV strain isolated from the stool sample of a patient with acute gastroenteritis from South Korea was amplified using three pairs of previously designed primers and seven newly designed primers. The recombinant HAstV was 6757-bp long and contained three sequential open reading frames (ORFs), designated as ORF1a (2781 bp), ORF1b (1548 bp), and ORF2 (2349 bp). Our findings suggested that a recombination event had occurred between ORF1b and ORF2 of the isolated strain, with a recombination breakpoint at 4081 bp. To our knowledge, this is the first study to reveal the complete nucleotide sequence of a recombinant HAstV strain from South Korea. Our study findings might be useful for identifying other recombinant HAstV strains and for developing vaccines against this pathogenic virus.
Yu, Jeong-Nam; Kim, Byung-Jik; Kim, Changmu; Yeo, Joo-Hong; Kim, Soonok
The Black star fat minnow (Rhynchocypris semotilus) is an endemic and critically endangered freshwater fish in Korea. Its genome was 16 605 bp long and consisted of 13 protein-coding genes (PCG), two rRNA genes, 22 tRNA genes, and a control region. The gene order and the composition of R. semotilus were similar to that of most other vertebrates. Four overlapping regions in ATP8/ATP6, ATP6/COX3, ND4L/ND4, and ND5/ND6, among the 13 PCGs were found. The control region was located between the tRNA-Pro and tRNA-Phe genes and was determined to be 935 bp in length with the 3' end containing a 12 TA-repeat sequence. Phylogenetic analysis suggested that R. semotilus is most closely related to R. oxycephalus.
Houldcroft, Charlotte J; Underdown, Simon J
High quality Altai Neanderthal and Denisovan genomes are revealing which regions of archaic hominin DNA have persisted in the modern human genome. A number of these regions are associated with response to infection and immunity, with a suggestion that derived Neanderthal alleles found in modern Europeans and East Asians may be associated with autoimmunity. As such Neanderthal genomes are an independent line of evidence of which infectious diseases Neanderthals were genetically adapted to. Sympathetically, human genome adaptive introgression is an independent line of evidence of which infectious diseases were important for AMH coming in to Eurasia and interacting with Neanderthals. The Neanderthals and Denisovans present interesting cases of hominin hunter-gatherers adapted to a Eurasian rather than African infectious disease package. Independent sources of DNA-based evidence allow a re-evaluation of the first epidemiologic transition and how infectious disease affected Pleistocene hominins. By combining skeletal, archaeological and genetic evidence from modern humans and extinct Eurasian hominins, we question whether the first epidemiologic transition in Eurasia featured a new package of infectious diseases or a change in the impact of existing pathogens. Coupled with pathogen genomics, this approach supports the view that many infectious diseases are pre-Neolithic, and the list continues to expand. The transfer of pathogens between hominin populations, including the expansion of pathogens from Africa, may also have played a role in the extinction of the Neanderthals and offers an important mechanism to understand hominin-hominin interactions well back beyond the current limits for aDNA extraction from fossils alone. Am J Phys Anthropol 160:379-388, 2016. © 2016 Wiley Periodicals, Inc.
Han, Myung Guk; Jung Sang, Ryou; Jeong, Young Eui; Ju, Young Ran; Cho, Jung Eun; Park, Jun-Sun
Objectives Human rabies is a reemerging infectious disease in Korea. There was no human rabies case for 14 years until the disease had reoccurred in 1999. To prevent occurrence of human rabies, surveillance for animal bite patients in rabies endemic areas in Korea was conducted since 2005 as a part of a human rabies control program. The animal bite cases were analyzed to determine whether patients were treated according to the post-exposure prophylaxis (PEP) guideline of the Korea Centers for Disease Control and Prevention. Methods Information of animal bite cases that occurred from 2005 to 2009 in rabies high-risk regions were collected by cooperation with Regional Public Health Centers in 18 cities/districts of rabies endemic areas. Results A total of 2458 animal bite cases were reported. Dogs accounted for 86% of animal bites and 67% of the animals were not vaccinated against rabies virus. For PEP, among rabies-vaccinated animals, 92.7% were observed for clinical signs and 1.4% underwent necropsy. Among unvaccinated animals, 72.7% were observed for clinical signs and 4.1% underwent necropsy. The remaining animals were not available for examination. Of the animal bite patients, 32.5% received PEP and 51.6% were treated by first aid or by washing the wound. Conclusions Given that no human rabies cases were reported since 2005 and animal rabies was continuously reported in endemic areas of Korea, the human rabies control program implemented in 2005 appears to have a significant role in the prevention and control of human rabies. PMID:24159481
Bayliss, Sion C; Verner-Jeffreys, David W; Bartie, Kerry L; Aanensen, David M; Sheppard, Samuel K; Adams, Alexandra; Feil, Edward J
Aquaculture is the fastest growing food-producing sector, and the sustainability of this industry is critical both for global food security and economic welfare. The management of infectious disease represents a key challenge. Here, we discuss the opportunities afforded by whole genome sequencing of bacterial and viral pathogens of aquaculture to mitigate disease emergence and spread. We outline, by way of comparison, how sequencing technology is transforming the molecular epidemiology of pathogens of public health importance, emphasizing the importance of community-oriented databases and analysis tools.
Bayliss, Sion C.; Verner-Jeffreys, David W.; Bartie, Kerry L.; Aanensen, David M.; Sheppard, Samuel K.; Adams, Alexandra; Feil, Edward J.
Aquaculture is the fastest growing food-producing sector, and the sustainability of this industry is critical both for global food security and economic welfare. The management of infectious disease represents a key challenge. Here, we discuss the opportunities afforded by whole genome sequencing of bacterial and viral pathogens of aquaculture to mitigate disease emergence and spread. We outline, by way of comparison, how sequencing technology is transforming the molecular epidemiology of pathogens of public health importance, emphasizing the importance of community-oriented databases and analysis tools. PMID:28217117
History of pneumonia is a strong risk factor for chronic obstructive pulmonary disease (COPD) exacerbation in South Korea: the Epidemiologic review and Prospective Observation of COPD and Health in Korea (EPOCH) study
Hwang, Yong Il; Lee, Sang Haak; Yoo, Jee Hong; Jung, Bock Hyun; Yoo, Kwang Ha; Na, Moon Jun; Lee, Jong Deog; Park, Myung Jae; Jung, Chi Young; Shim, Jae Jeong; Kim, Kyung Chan; Kim, Yeon Jae; Choi, Hye Sook; Choi, Ik Su; Lee, Choon-Taek; Lee, Sang Do; Kim, Do Jin; Uh, Soo-Taek; Lee, Ho Sung; Kim, Young Sam; Lee, Kwan Ho; Ra, Seung Won; Kim, Hak Ryul; Choi, Soo Jeon; Park, In Won; Park, Yong Bum; Park, So Young; Lee, Jaehee
Background In South Korea, chronic obstructive pulmonary disease (COPD) is one of the ten leading causes of death. COPD exacerbations are significantly associated with mortality in COPD patients. This study was conducted to investigate the epidemiology of COPD in South Korea, specifically the clinical characteristics of South Korean COPD patients, the COPD exacerbation rate and the risk factors associated with COPD exacerbations. Methods This study covers a 2-year interval. One year was data collected retrospectively and the second year was prospectively obtained data. Results A total of 1,114 subjects were enrolled in the study. These subjects were observed for a period of 1 year from the enrollment, and a total of 920 subjects completed the study. A total of 1,357 COPD exacerbations occurred in 711 subjects (63.8%) out of the total of 1,114 subjects during the study period of 2 years. Multivariate logistic regression results showed that if patients had had a pneumonia before the retrospective year of analysis, they had a 18 times greater chance of having an exacerbation during the prospective year when other variables were controlled. Also, the subjects who had a history of two or more exacerbations during the retrospective year were approximately 6 times more likely to experience the COPD exacerbation compared to those who did not. Conclusions This study examined the demographic and clinical characteristics of South Korean COPD patients and found that a history of pneumonia and two or more occurrences of exacerbation within 1 year was significantly associated with a higher rate of COPD exacerbation. PMID:26793342
Park, Dae Won; Chun, Byung Chul; Kim, June Myung; Sohn, Jang Wook; Peck, Kyong Ran; Kim, Yang Soo; Choi, Young Hwa; Choi, Jun Yong; Kim, Sang Il; Eom, Joong Sik; Kim, Hyo Youl; Song, Joon Young; Song, Young Goo; Choi, Hee Jung; Kim, Min Ja
A prospective multicenter observational study was performed to investigate the epidemiology and outcomes of community-acquired severe sepsis and septic shock. Subjects included 1,192 adult patients admitted to the 22 participating intensive care units (ICUs) of 12 university hospitals in the Korean Sepsis Registry System from April, 2005 through February, 2009. Male accounted for 656 (55%) patients. Mean age was 65.0 ± 14.2 yr. Septic shock developed in 740 (62.1%) patients. Bacteremia was present in 422 (35.4%) patients. The 28-day and in-hospital mortality rates were 23.0% and 28.0%, respectively. Men were more likely to have comorbid illnesses and acute organ dysfunctions, and had higher mortality and clinical severity compared to women. While respiratory sources of sepsis were common in men, urinary sources were predominant in women. In the multivariate logistic regression analysis, cancer (odds ratio 1.89; 95% confidence interval 1.13-3.17), urinary tract infection (0.25; 0.13-0.46), APACHE II score (1.05; 1.02-1.09), SOFA score on day 1 (1.13; 1.06-1.21) and metabolic dysfunction (2.24, 1.45-3.45) were independent clinical factors for gender-related in-hospital mortality. This study provided epidemiological and clinical characteristics of community-acquired severe sepsis and septic shock in ICUs in Korea, and demonstrated the impact of clinical factors on gender difference in mortality.
We analyzed the causes leading to total hip arthroplasty (THA), aimed to clarify the incidence of femoroacetabular impingement (FAI) among the causes, and compared the incidence in Korea with those in other countries. From January 2000 to December 2014, 1,206 hips of 818 patients who underwent primary THA at our institute were reviewed retrospectively in terms of radiographs and electronic charts. The radiographs and radiographic parameters were reviewed and measured by 2 of the authors, who are orthopedic surgeons. Patients were categorized in terms of the causes leading to THA as primary osteoarthritis (OA), rheumatoid arthritis (RA), posttraumatic arthritis, post infectious arthritis, avascular necrosis (AVN) of the femoral head, fracture of the femoral head or neck, ankylosing spondylitis (AS), developmental dysplasia of the hip (DDH), Legg-Calvé-Perthes disease (LCPD), FAI, and others. There were 32 patients (3.91%) in the primary OA group, 41 (5.01%) in the RA group, 84 (10.27%) in the posttraumatic arthritis group, 39 (4.77%) in the post infectious arthritis group, 365 (44.62%) in the AVN group, 39 (4.77%) in the fracture group, 21 (2.57%) in the AS group, 52 (6.36%) in the DDH group, 71 (8.68%) in the LCPD group, 52 (6.36%) in the FAI group, and 22 (2.69%) in the ‘other’ group. The causes leading to THA in Korea differ from those in Western countries. FAI could be causes of severe secondary OA that requires THA in Korea, therefore symptomatic FAI should not be neglected. PMID:28244282
Grange, Zoë L; Biggs, Patrick J; Rose, Shanna P; Gartrell, Brett D; Nelson, Nicola J; French, Nigel P
Translocation and isolation of threatened wildlife in new environments may have unforeseen consequences on pathogen transmission and evolution in host populations. Disease threats associated with intensive conservation management of wildlife remain speculative without gaining an understanding of pathogen dynamics in meta-populations and how location attributes may determine pathogen prevalence. We determined the prevalence and population structure of an opportunistic pathogen, Salmonella, in geographically isolated translocated sub-populations of an endangered New Zealand flightless bird, the takahe (Porphyrio hochstetteri). Out of the nine sub-populations tested, Salmonella was only isolated from takahe living on one private island. The apparent prevalence of Salmonella in takahe on the private island was 32% (95% CI 13-57%), with two serotypes, Salmonella Mississippi and Salmonella houtenae 40:gt-, identified. Epidemiological investigation of reservoirs on the private island and another island occupied by takahe identified environmental and reptile sources of S. Mississippi and S. houtenae 40:gt- on the private island. Single nucleotide polymorphism analysis of core genomes revealed low-level diversity among isolates belonging to the same serotype and little differentiation according to host and environmental source. The pattern observed may be representative of transmission between sympatric hosts and environmental sources, the presence of a common unsampled source, and/or evidence of a recent introduction into the ecosystem. This study highlights how genomic epidemiology can be used to ascertain and understand disease dynamics to inform the management of disease threats in endangered wildlife populations.
Jans, Christoph; Meile, Leo; Lacroix, Christophe; Stevens, Marc J A
The Streptococcus bovis/Streptococcus equinus complex (SBSEC) is a group of human and animal derived streptococci that are commensals (rumen and gastrointestinal tract), opportunistic pathogens or food fermentation associates. The classification of SBSEC has undergone massive changes and currently comprises 7 (sub)species grouped into four branches based on sequences identities: the Streptococcus gallolyticus, the Streptococcus equinus, the Streptococcus infantarius and the Streptococcus alactolyticus branch. In animals, SBSEC are causative agents for ruminal acidosis, potentially laminitis and infective endocarditis (IE). In humans, a strong association was established between bacteraemia, IE and colorectal cancer. Especially the SBSEC-species S. gallolyticus subsp. gallolyticus is an emerging pathogen for IE and prosthetic joint infections. S. gallolyticus subsp. pasteurianus and the S. infantarius branch are further associated with biliary and urinary tract infections. Knowledge on pathogenic mechanisms is so far limited to colonization factors such as pili and biofilm formation. Certain strain variants of S. gallolyticus subsp. macedonicus and S. infantarius subsp. infantarius are associated with traditional dairy and plant-based food fermentations and display traits suggesting safety. However, due to their close relationship to virulent strains, their use in food fermentation has to be critically assessed. Additionally, implementing accurate and up-to-date taxonomy is critical to enable appropriate treatment of patients and risk assessment of species and strains via recently developed multilocus sequence typing schemes to enable comparative global epidemiology. Comparative genomics revealed that SBSEC strains harbour genomics islands (GI) that seem acquired from other streptococci by horizontal gene transfer. In case of virulent strains these GI frequently encode putative virulence factors, in strains from food fermentation the GI encode functions that are
Yang, Yunxing; Wang, Jianfeng; Fu, Ying; Ruan, Zhi; Yu, Yunsong
Clinical infections caused by Acinetobacter spp. have increasing public health concerns because of their global occurrence and ability to acquire multidrug resistance. Acinetobacter calcoaceticus-Acinetobacter baumannii (ACB) complex encompasses A. calcoaceticus, A. baumannii, A. pittii (formerly genomic species 3), and A nosocomial (formerly genomic species 13TU), which are predominantly responsible for clinical pathogenesis in the Acinetobacter genus. In our previous study, a putative novel species isolated from 385 non-A. baumannii spp. strains based on the rpoB gene phylogenetic tree was reported. Here, the putative novel species was identified as A. seifertii based on the whole-genome phylogenetic tree. A. seifertii was recognized as a novel member of the ACB complex and close to A. baumannii and A. nosocomials. Furthermore, we studied the characteristics of 10 A. seifertii isolates, which were distributed widely in 6 provinces in China and mainly caused infections in the elderly or children. To define the taxonomic status and characteristics, the biochemical reactions, antimicrobial susceptibility testing, pulsed field gel electrophoresis (PFGE), multilocus sequence typing (MLST), and whole-genome sequence analysis were performed. The phenotypic characteristics failed to distinguish A. serfertii from other species in the ACB complex. Most of the A. seifertii isolates were susceptible to antibiotics commonly used for nosocomial Acinetobacter spp. infections, but one isolate (strain A362) was resistant to ampicillin/sulbactam, ceftazidime and amikacin. The different patterns of MLST and PFGE suggested that the 10 isolates were not identical and lacked clonal relatedness. Our study reported for the first time the molecular epidemiological and genomic features of widely disseminated A. seifertii in China. These observations could enrich the knowledge of infections caused by non-A. baumannii and may provide a scientific basis for future clinical treatment.
Katz, Lee S; Griswold, Taylor; Williams-Newkirk, Amanda J; Wagner, Darlene; Petkau, Aaron; Sieffert, Cameron; Van Domselaar, Gary; Deng, Xiangyu; Carleton, Heather A
Modern epidemiology of foodborne bacterial pathogens in industrialized countries relies increasingly on whole genome sequencing (WGS) techniques. As opposed to profiling techniques such as pulsed-field gel electrophoresis, WGS requires a variety of computational methods. Since 2013, United States agencies responsible for food safety including the CDC, FDA, and USDA, have been performing whole-genome sequencing (WGS) on all Listeria monocytogenes found in clinical, food, and environmental samples. Each year, more genomes of other foodborne pathogens such as Escherichia coli, Campylobacter jejuni, and Salmonella enterica are being sequenced. Comparing thousands of genomes across an entire species requires a fast method with coarse resolution; however, capturing the fine details of highly related isolates requires a computationally heavy and sophisticated algorithm. Most L. monocytogenes investigations employing WGS depend on being able to identify an outbreak clade whose inter-genomic distances are less than an empirically determined threshold. When the difference between a few single nucleotide polymorphisms (SNPs) can help distinguish between genomes that are likely outbreak-associated and those that are less likely to be associated, we require a fine-resolution method. To achieve this level of resolution, we have developed Lyve-SET, a high-quality SNP pipeline. We evaluated Lyve-SET by retrospectively investigating 12 outbreak data sets along with four other SNP pipelines that have been used in outbreak investigation or similar scenarios. To compare these pipelines, several distance and phylogeny-based comparison methods were applied, which collectively showed that multiple pipelines were able to identify most outbreak clusters and strains. Currently in the US PulseNet system, whole genome multi-locus sequence typing (wgMLST) is the preferred primary method for foodborne WGS cluster detection and outbreak investigation due to its ability to name standardized
Katz, Lee S.; Griswold, Taylor; Williams-Newkirk, Amanda J.; Wagner, Darlene; Petkau, Aaron; Sieffert, Cameron; Van Domselaar, Gary; Deng, Xiangyu; Carleton, Heather A.
Modern epidemiology of foodborne bacterial pathogens in industrialized countries relies increasingly on whole genome sequencing (WGS) techniques. As opposed to profiling techniques such as pulsed-field gel electrophoresis, WGS requires a variety of computational methods. Since 2013, United States agencies responsible for food safety including the CDC, FDA, and USDA, have been performing whole-genome sequencing (WGS) on all Listeria monocytogenes found in clinical, food, and environmental samples. Each year, more genomes of other foodborne pathogens such as Escherichia coli, Campylobacter jejuni, and Salmonella enterica are being sequenced. Comparing thousands of genomes across an entire species requires a fast method with coarse resolution; however, capturing the fine details of highly related isolates requires a computationally heavy and sophisticated algorithm. Most L. monocytogenes investigations employing WGS depend on being able to identify an outbreak clade whose inter-genomic distances are less than an empirically determined threshold. When the difference between a few single nucleotide polymorphisms (SNPs) can help distinguish between genomes that are likely outbreak-associated and those that are less likely to be associated, we require a fine-resolution method. To achieve this level of resolution, we have developed Lyve-SET, a high-quality SNP pipeline. We evaluated Lyve-SET by retrospectively investigating 12 outbreak data sets along with four other SNP pipelines that have been used in outbreak investigation or similar scenarios. To compare these pipelines, several distance and phylogeny-based comparison methods were applied, which collectively showed that multiple pipelines were able to identify most outbreak clusters and strains. Currently in the US PulseNet system, whole genome multi-locus sequence typing (wgMLST) is the preferred primary method for foodborne WGS cluster detection and outbreak investigation due to its ability to name standardized
Panda, Preetinanda; Taylor, Robert; Pitman, Andrew R.
ABSTRACT Pectobacterium carotovorum subsp. actinidiae is the causal agent of summer canker in kiwifruit plants in South Korea. We report here the draft genome sequences of two P. carotovorum subsp. actinidiae strains, ICMP 19971 and ICMP 19972, which were originally isolated from Actinidia chinensis with symptoms of summer canker. These genome sequences will aid in the identification of genetic traits associated with their unusual capacity to cause canker and help understanding of the threat these exotic enterobacteria pose to the New Zealand kiwifruit industry. PMID:28385839
Kim, Chang Keun; Choi, Jungi; Callaway, Zak; Kim, Hyo Bin; Chung, Ju Young; Koh, Young-Yull; Shin, Bo Moon
Human metapneumovirus (HMPV) shares clinical and epidemiological characteristics with well-known respiratory syncytial virus (RSV). The aim of this study was to investigate the clinical and epidemiological differences between HMPV- and RSV-induced wheezing illnesses. A total of 1,008 nasopharyngeal aspirate specimens was collected from 1,008 pediatric patients hospitalized with acute respiratory tract infection at Inje University Sanggye Paik Hospital from December 2003 to April 2008, and tested for seven common respiratory viruses. Conditions classified as wheezing illness were bronchiolitis, reactive airways disease, and bronchial asthma. HMPV caused a significantly lower proportion of wheezing illness when compared to RSV (48.1% vs. 82.2%, P<0.05). HMPV-induced wheezing illness occurred predominantly in older patients when compared to RSV patients (P<0.001). RSV infections peaked in the fall and winter followed by peaks of HMPV infection in winter and spring. Eosinophil counts were significantly higher (P<0.01) in RSV patients when compared to HMPV patients. These results show that human metapneumovirus patients exhibit several different clinical and epidemiological characteristics, such as higher proportion of wheezing illness, age and seasonal incidence, and eosinophil counts, when compared to RSV patients.
Yong, Ji Hyun; Lee, Yeong Seon; Yoo, Jung Sik; Yong, Dongeun; Hong, Seong Geun; D'Souza, Roshan; Thomson, Kenneth S.; Lee, Kyungwon; Chong, Yunsop
We analyzed the whole genome sequence and resistome of the outbreak Klebsiella pneumoniae strain MP14 and compared it with those of K. pneumoniae carbapenemase- (KPC-) producing isolates that showed high similarity in the NCBI genome database. A KPC-2-producing multidrug-resistant (MDR) K. pneumoniae clinical isolate was obtained from a patient admitted to a Korean hospital in 2011. The strain MP14 was resistant to all tested β-lactams including monobactam, amikacin, levofloxacin, and cotrimoxazole, but susceptible to tigecycline and colistin. Resistome analysis showed the presence of β-lactamase genes including blaKPC-2, blaSHV-11, blaTEM-169, and blaOXA-9. MP14 also possessed aac(6′-)Ib, aadA2, and aph(3′-)Ia as aminoglycoside resistance-encoding genes, mph(A) for macrolides, oqxA and oqxB for quinolone, catA1 for phenicol, sul1 for sulfonamide, and dfrA12 for trimethoprim. Both SNP tree and cgMLST analysis showed the close relatedness with the KPC producers (KPNIH strains) isolated from an outbreak in the USA and colistin-resistant strains isolated in Italy. The plasmid-scaffold genes in plasmids pKpQil, pKpQil-IT, pKPN3, or pKPN-IT were identified in MP14, KPNIH, and Italian strains. The KPC-2-producing MDR K. pneumoniae ST258 stain isolated in Korea was highly clonally related with MDR K. pneumoniae strains from the USA and Italy. Global spread of KPC-producing K. pneumoniae is a worrying phenomenon. PMID:25105122
Lee, Yangsoon; Kim, Bong-Soo; Chun, Jongsik; Yong, Ji Hyun; Lee, Yeong Seon; Yoo, Jung Sik; Yong, Dongeun; Hong, Seong Geun; D'Souza, Roshan; Thomson, Kenneth S; Lee, Kyungwon; Chong, Yunsop
We analyzed the whole genome sequence and resistome of the outbreak Klebsiella pneumoniae strain MP14 and compared it with those of K. pneumoniae carbapenemase- (KPC-) producing isolates that showed high similarity in the NCBI genome database. A KPC-2-producing multidrug-resistant (MDR) K. pneumoniae clinical isolate was obtained from a patient admitted to a Korean hospital in 2011. The strain MP14 was resistant to all tested β-lactams including monobactam, amikacin, levofloxacin, and cotrimoxazole, but susceptible to tigecycline and colistin. Resistome analysis showed the presence of β-lactamase genes including bla KPC-2, bla SHV-11, bla TEM-169, and bla OXA-9. MP14 also possessed aac(6'-)Ib, aadA2, and aph(3'-)Ia as aminoglycoside resistance-encoding genes, mph(A) for macrolides, oqxA and oqxB for quinolone, catA1 for phenicol, sul1 for sulfonamide, and dfrA12 for trimethoprim. Both SNP tree and cgMLST analysis showed the close relatedness with the KPC producers (KPNIH strains) isolated from an outbreak in the USA and colistin-resistant strains isolated in Italy. The plasmid-scaffold genes in plasmids pKpQil, pKpQil-IT, pKPN3, or pKPN-IT were identified in MP14, KPNIH, and Italian strains. The KPC-2-producing MDR K. pneumoniae ST258 stain isolated in Korea was highly clonally related with MDR K. pneumoniae strains from the USA and Italy. Global spread of KPC-producing K. pneumoniae is a worrying phenomenon.
Popovich, Kyle J.; Snitkin, Evan; Green, Stefan J.; Aroutcheva, Alla; Hayden, Mary K.; Hota, Bala; Weinstein, Robert A.
Background. In a community, it is unknown what factors account for transmission of methicillin-resistant Staphylococcus aureus (MRSA). We integrated whole genome sequencing (WGS) and epidemiologic data to identify factors associated with MRSA transmission networks in an urban community. Methods. WGS was performed on colonizing USA300 MRSA isolates from 74 individuals within 72 hours of admission to a public hospital in Chicago, IL. Single nucleotide variants (SNVs) were used to reconstruct the phylogeny of sequenced isolates, and epidemiologic data was overlaid to identify factors associated with transmission networks. Results. The maximum within-patient SNV difference for an individual with multisite colonization was 41 SNVs, with no systematic divergence among body sites. We observed a minimum of 7 SNVs and maximum of 153 SNVs between isolates from different individuals. We identified 4 pairs of individuals whose isolates were within 40 SNVs of each other. Putting our isolates in the context of previously sequenced USA300 isolates from other communities, we identified a 13-member group and two 4-member groups that represent samples from putative local transmission networks. Individuals in these groups were more likely to be African American, to be human immunodeficiency virus–infected, to reside in high detainee release areas, and to be current users of illicit drugs. Conclusions. Using WGS, we observed potential transmission networks in an urban community and that certain epidemiologic factors were associated with inclusion in these networks. Future work with contact tracing and advanced molecular diagnostics may allow for identification of MRSA “epicenters” in the community where interventions can be targeted. PMID:26347509
Tyson, Gregory H; Li, Cong; Ayers, Sherry; McDermott, Patrick F; Zhao, Shaohua
For Enterobacteriaceae such as Salmonella spp. and Escherichia coli, no unified interpretive resistance criteria exist for streptomycin, an epidemiologically important antibiotic. As part of the National Antimicrobial Resistance Monitoring System, we had previously used a minimum inhibitory concentration of ≥ 64 μg mL(-1) as an epidemiological cutoff value (ECV) to define non-wild-type isolates. To identify whether this ECV correlated with genetic determinants of resistance, we performed whole-genome sequencing of 463 Salmonella and E. coli isolates to identify streptomycin resistance genotypes. From this analysis, we found that using a streptomycin resistance breakpoint of ≥ 64 μg mL(-1) classified over 20% of strains possessing aadA or strA/strB resistance genes as wild-type. Therefore, to improve the concordance between genotypic and phenotypic data, we propose reducing the phenotypic cutoff values to ≥ 32 μg mL(-1) for both Salmonella and E. coli, to be used widely as ECVs to categorize non-wild-type isolates.
Grad, Yonatan H; Lipsitch, Marc; Feldgarden, Michael; Arachchi, Harindra M; Cerqueira, Gustavo C; Fitzgerald, Michael; Godfrey, Paul; Haas, Brian J; Murphy, Cheryl I; Russ, Carsten; Sykes, Sean; Walker, Bruce J; Wortman, Jennifer R; Young, Sarah; Zeng, Qiandong; Abouelleil, Amr; Bochicchio, James; Chauvin, Sara; Desmet, Timothy; Gujja, Sharvari; McCowan, Caryn; Montmayeur, Anna; Steelman, Scott; Frimodt-Møller, Jakob; Petersen, Andreas M; Struve, Carsten; Krogfelt, Karen A; Bingen, Edouard; Weill, François-Xavier; Lander, Eric S; Nusbaum, Chad; Birren, Bruce W; Hung, Deborah T; Hanage, William P
The degree to which molecular epidemiology reveals information about the sources and transmission patterns of an outbreak depends on the resolution of the technology used and the samples studied. Isolates of Escherichia coli O104:H4 from the outbreak centered in Germany in May-July 2011, and the much smaller outbreak in southwest France in June 2011, were indistinguishable by standard tests. We report a molecular epidemiological analysis using multiplatform whole-genome sequencing and analysis of multiple isolates from the German and French outbreaks. Isolates from the German outbreak showed remarkably little diversity, with only two single nucleotide polymorphisms (SNPs) found in isolates from four individuals. Surprisingly, we found much greater diversity (19 SNPs) in isolates from seven individuals infected in the French outbreak. The German isolates form a clade within the more diverse French outbreak strains. Moreover, five isolates derived from a single infected individual from the French outbreak had extremely limited diversity. The striking difference in diversity between the German and French outbreak samples is consistent with several hypotheses, including a bottleneck that purged diversity in the German isolates, variation in mutation rates in the two E. coli outbreak populations, or uneven distribution of diversity in the seed populations that led to each outbreak.
Jang, Yo-Soon; Park, Kwang-Jae; Kim, Ki-Yong; Kim, Sung
Due to variations in coloration as well as other morphological features, the identification of Sebastes pachycephalus has been problematic. The complete mitogenome of S. pachycephalus was acquired using next-generation sequencing. The full genome was 16,415 base pairs (bp) in length, assembling two rRNAs, 22 tRNAs, one control region and 13 protein-coding genes (PCGs). The genome constitutes 27.9% A, 26.3% T, 17.2% G and 28.5% C, showing a slight AT bias (54.2%). All PCGs start with an ATG initial codon except COX1, which contains GTG. Most PCG stop codons were TAA, except for ND1 and ND3 (TAG) and Cytb (incomplete termination codon, T). All tRNAs showed the typical cloverleaf structure, except tRNA(Ser(AGY)), which lacks the DHU arm. The complete mitogenome of S. pachycephalus will help further identification and speciation analyses.
Kim, Eu Suk; Kim, Hong Bin; Kim, Gayeon; Kim, Kye-Hyung; Park, Kyung-Hwa; Lee, Shinwon; Choi, Young Hwa; Yi, Jongyoun; Kim, Chung Jong; Song, Kyoung-Ho; Choe, Pyoeng Gyun; Kim, Nam-Joong; Lee, Yeong-Seon; Oh, Myoung-Don
Successful empirical therapy of Staphylococcus aureus infections requires the ability to predict methicillin resistance. Our aim was to identify predictors of methicillin resistance in community-onset (CO) invasive S. aureus infections. Sixteen hospitals across Korea participated in this study from May to December 2012. We prospectively included cases of S. aureus infection in which S. aureus was isolated from sterile clinical specimens ≤ 72 hours after hospitalization. Clinical and epidemiological data were gathered and compared in methicillin-resistant S. aureus (MRSA) and methicillin-susceptible S. aureus (MSSA) cases. Community-associated (CA) infections were defined as in previous studies. In total, there were 786 cases of community-onset S. aureus infection, 102 (13.0%) of which were CA-MRSA. In addition to known risk factors, exposure to 3rd generation cephalosporins in the past 6 months [odds ratio (OR), 1.922; 95% confidence interval (CI), 1.176-3.142] and close contact with chronically ill patients in the past month (OR, 2.647; 95% CI, 1.189-5.891) were independent risk factors for MRSA infection. However, no clinical predictors of CA-MRSA were identified. Methicillin resistance, CO infection, and appropriateness of empirical antibiotics were not significantly related to 30-day mortality. MRSA infection should be suspected in patients recently exposed to 3rd generation cephalosporins or chronically-ill patients. There were no reliable predictors of CA-MRSA infection, and mortality was not affected by methicillin resistance.
Lee, Choong Bum; Choe, Hyun-Sop; Hwang, Seong-Jin; Lee, Seung-Ju; Cho, Yong-Hyun
As viral sexually transmitted infections (STIs) are hard to cure completely and because they recur frequently, the management of patients and the prevention of the spread of viral STIs are important, rather than focusing on their treatment, unlike the focus for bacterial STIs. Thus, their prevalence and epidemiological characteristics should be investigated first. This study examined the prevalence of genital herpes and condyloma acuminata in patients visiting urologic and gynecologic clinics and evaluated the epidemiological characteristics of these diseases through questionnaire surveys. Out of 167,767 patients, 1,585 were reported to have genital herpes and condyloma acuminata, and the prevalences of the two diseases were 0.58 and 0.37%, respectively. The percentage of patients with viral STIs as a proportion of the total number of patients with STIs including bacterial STIs, was 35.6%. While the prevalence of genital herpes was relatively higher in middle-aged patients, that of condyloma acuminata was observed to be higher in relatively young patients. Among the patients participating in the questionnaire survey, 39.5 and 21.0% responded that they had experienced recurrence of genital herpes and condyloma acuminata, respectively. In conclusion, because the prevalences of genital herpes and condyloma acuminata as viral STIs were not trivial compared to that of bacterial STIs, and because of their frequent recurrence, policies adjusted to the characteristics of these viral STIs and more studies on the management of recurrence are necessary.
Jeon, Hyeong-Kyu; Kim, Kyu-Heon; Chai, Jong-Yil; Yang, Hyun-Jong; Rim, Han-Jong; Eom, Keeseon S
Taeniasis has been known as one of the prevalent parasitic infections in Korea. Until recently, Taenia saginata had long been considered a dominant, and widely distributed species but epidemiological profiles of human Taenia species in Korea still remain unclear. In order to better understand distribution patterns of human Taenia tapeworms in Korea, partial nucleotide sequences of mitochondrial cox1 and ITS2 (internal transcribed spacer 2) were determined, along with morphological examinations, on 68 Taenia specimens obtained from university museum collections deposited since 1935. Genomic DNA was extracted from formalin-preserved specimens. Phylogenetic relationships among the genotypes (cox1 haplotype) detected in this study were inferred using the neighbor-joining method as a tree building method. Morphological and genetic analyses identified 3 specimens as T. solium, 51 specimens as T. asiatica, and 14 specimens as T. saginata. Our results indicate that all 3 Taenia tapeworms are sympatrically distributed in Korea with T. asiatica dominating over T. saginata and T. solium.
Shim, Unjin; Kim, Han-Na; Sung, Yeon-Ah
Metabolic syndrome (MetS) is a complex disorder related to insulin resistance, obesity, and inflammation. Genetic and environmental factors also contribute to the development of MetS, and through genome-wide association studies (GWASs), important susceptibility loci have been identified. However, GWASs focus more on individual single-nucleotide polymorphisms (SNPs), explaining only a small portion of genetic heritability. To overcome this limitation, pathway analyses are being applied to GWAS datasets. The aim of this study is to elucidate the biological pathways involved in the pathogenesis of MetS through pathway analysis. Cohort data from the Korea Associated Resource (KARE) was used for analysis, which include 8,842 individuals (age, 52.2 ± 8.9 years; body mass index, 24.6 ± 3.2 kg/m2). A total of 312,121 autosomal SNPs were obtained after quality control. Pathway analysis was conducted using Meta-analysis Gene-Set Enrichment of Variant Associations (MAGENTA) to discover the biological pathways associated with MetS. In the discovery phase, SNPs from chromosome 12, including rs11066280, rs2074356, and rs12229654, were associated with MetS (p < 5 × 10-6), and rs11066280 satisfied the Bonferroni-corrected cutoff (unadjusted p < 1.38 × 10-7, Bonferroni-adjusted p < 0.05). Through pathway analysis, biological pathways, including electron carrier activity, signaling by platelet-derived growth factor (PDGF), the mitogen-activated protein kinase kinase kinase cascade, PDGF binding, peroxisome proliferator-activated receptor (PPAR) signaling, and DNA repair, were associated with MetS. Through pathway analysis of MetS, pathways related with PDGF, mitogen-activated protein kinase, and PPAR signaling, as well as nucleic acid binding, protein secretion, and DNA repair, were identified. Further studies will be needed to clarify the genetic pathogenesis leading to MetS. PMID:25705158
Song, Joon Young; Hwang, In Sook; Eom, Joong Sik; Cheong, Hee Jin; Bae, Won Ki; Park, Yong Ho
Background To assess the possibility of VRE transmission from animals to humans, we studied the prevalence of vancomycin-resistant enterococci (VRE) in farm animals, raw chicken meat, and healthy people. We then determined the molecular relatedness of VRE isolates between animals and humans in Korea. Methods We aimed to isolate VRE from 150 enterococci specimens of farm animals, 15 raw chicken meat samples, and stools from 200 healthy people. Species differentiation was done with conventional biochemical tests. Vancomycin resistance genotyping was done by polymerase chain reaction (PCR). Using the agar dilution method, antimicrobial susceptibility was tested for 8 antimicrobials and pulsed-field gel electrophoresis (PFGE) was done to evaluate the molecular relatedness of VRE isolates. Results The prevalence of VRE was 14.7% (22/150) in farm animal specimens, 1% (2/200) in healthy people, and 60% (9/15) in raw chicken meat. Of 22 animal VRE isolates, 1 vanA E. faecium, 15 vanC1 E. gallinarum, and 6 vanC2 E. casseliflavus were identified. All of the 9 VRE from raw chicken meat and all of the 20 clinical VRE strains were vanA E. faecium. However, in healthy people, only 2 vanC2 E. casseliflavus were isolated. These showed low-level resistance to vancomycin and susceptibility to teicoplanin. However, 9 VRE strains from raw chicken meat had high-level resistance to vancomycin (MIC50,90: >128 µg/mL), teicoplanin (MIC50,90: >128 µg/mL), ampicillin (MIC50,90: >128 µg/mL), erythromycin (MIC50,90: >128 µg/mL), and tetracycline (MIC50,90: 128/>128 µg/mL). Conclusion This study demonstrated little evidence of VRE colonization in healthy people despite high recovery of VRE among raw chicken meat. It is suggested that there is little evidence of VRE transmission from animals to healthy people. However, we assumed that there exists the possibility of VRE contamination during the processing of chicken meat. PMID:15906954
Lee, Dong-Hun; Park, Jae-Keun; Yuk, Seong-Su; Erdene-Ochir, Tseren-Ochir; Kwon, Jung-Hoon; Lee, Joong-Bok; Park, Seung-Yong; Choi, In-Soo; Lee, Sang-Won; Song, Chang-Seon
In 2011, we isolated a natural recombinant H9N2 avian influenza virus from fecal droppings of bean goose (Anser fabalis) in Korea. Phylogenetic analyses showed that the A/bean goose/Korea/220/2011(H9N2) isolate is a reassortant of Eurasian and North American lineages of avian influenza virus. In addition, the complete genome sequence, including all 8 gene segments, was associated with Chinese H9N2 viruses isolated from wild birds in the Hunan East Dongting Lake National Nature Reserve. These data provide direct evidence for the exchange of avian influenza viruses between Korea and China via wild birds.
Hagiwara, Daisuke; Watanabe, Akira; Kamei, Katsuhiko; Goldman, Gustavo H.
Invasive aspergillosis is a life-threatening mycosis caused by the pathogenic fungus Aspergillus. The predominant causal species is Aspergillus fumigatus, and azole drugs are the treatment of choice. Azole drugs approved for clinical use include itraconazole, voriconazole, posaconazole, and the recently added isavuconazole. However, epidemiological research has indicated that the prevalence of azole-resistant A. fumigatus isolates has increased significantly over the last decade. What is worse is that azole-resistant strains are likely to have emerged not only in response to long-term drug treatment but also because of exposure to azole fungicides in the environment. Resistance mechanisms include amino acid substitutions in the target Cyp51A protein, tandem repeat sequence insertions at the cyp51A promoter, and overexpression of the ABC transporter Cdr1B. Environmental azole-resistant strains harboring the association of a tandem repeat sequence and punctual mutation of the Cyp51A gene (TR34/L98H and TR46/Y121F/T289A) have become widely disseminated across the world within a short time period. The epidemiological data also suggests that the number of Aspergillus spp. other than A. fumigatus isolated has risen. Some non-fumigatus species intrinsically show low susceptibility to azole drugs, imposing the need for accurate identification, and drug susceptibility testing in most clinical cases. Currently, our knowledge of azole resistance mechanisms in non-fumigatus Aspergillus species such as A. flavus, A. niger, A. tubingensis, A. terreus, A. fischeri, A. lentulus, A. udagawae, and A. calidoustus is limited. In this review, we present recent advances in our understanding of azole resistance mechanisms particularly in A. fumigatus. We then provide an overview of the genome sequences of non-fumigatus species, focusing on the proteins related to azole resistance mechanisms. PMID:27708619
Maraqa, Nizar F.; Cook, Robert L.; Johnson, Judith A.; Bailey, Christine; Wheeler, Sarah; Nolan, David; Rathore, Mobeen H.; Morris, J. Glenn; Salemi, Marco
Despite infection prevention efforts, neonatal intensive care unit (NICU) patients remain at risk of Methicillin-resistant Staphylococcus aureus (MRSA) infection. Modes of transmission for healthcare-associated (HA) and community-associated (CA) MRSA remain poorly understood and may vary by genotype, hindering the development of effective prevention and control strategies. From 2008–2010, all patients admitted to a level III NICU were screened for MRSA colonization, and all available isolates were spa-typed. Spa-type t008, the most prevalent CA- genotype in the United States, spa-type t045, a HA- related genotype, and a convenience sample of strains isolated from 2003–2011, underwent whole-genome sequencing and phylodynamic analysis. Patient risk factors were compared between colonized and noncolonized infants, and virulence and resistance genes compared between spa-type t008 and non-t008 strains. Epidemiological and genomic data were used to estimate MRSA importations and acquisitions through transmission reconstruction. MRSA colonization was identified in 9.1% (177/1940) of hospitalized infants and associated with low gestational age and birth weight. Among colonized infants, low gestational age was more common among those colonized with t008 strains. Our data suggest that approximately 70% of colonizations were the result of transmission events within the NICU, with the remainder likely to reflect importations of “outside” strains. While risk of transmission within the NICU was not affected by spa-type, patterns of acquisition and importation differed between t008 and t045 strains. Phylodynamic analysis showed the effective population size of spa-type t008 has been exponentially increasing in both community and hospital, with spa-type t008 strains possessed virulence genes not found among t045 strains; t045 strains, in contrast, appeared to be of more recent origin, with a possible hospital source. Our data highlight the importance of both intra
Johnson, Catherine; Drgon, Tomas; Liu, Qing-Rong; Zhang, Ping-Wu; Walther, Donna; Li, Chuan-Yun; Anthony, James C; Ding, Yulan; Eaton, William W; Uhl, George R
Background Dependences on addictive substances are substantially-heritable complex disorders whose molecular genetic bases have been partially elucidated by studies that have largely focused on research volunteers, including those recruited in Baltimore. Maryland. Subjects recruited from the Baltimore site of the Epidemiological Catchment Area (ECA) study provide a potentially-useful comparison group for possible confounding features that might arise from selecting research volunteer samples of substance dependent and control individuals. We now report novel SNP (single nucleotide polymorphism) genome wide association (GWA) results for vulnerability to substance dependence in ECA participants, who were initially ascertained as members of a probability sample from Baltimore, and compare the results to those from ethnically-matched Baltimore research volunteers. Results We identify substantial overlap between the home address zip codes reported by members of these two samples. We find overlapping clusters of SNPs whose allele frequencies differ with nominal significance between substance dependent vs control individuals in both samples. These overlapping clusters of nominally-positive SNPs identify 172 genes in ways that are never found by chance in Monte Carlo simulation studies. Comparison with data from human expressed sequence tags suggests that these genes are expressed in brain, especially in hippocampus and amygdala, to extents that are greater than chance. Conclusion The convergent results from these probability sample and research volunteer sample datasets support prior genome wide association results. They fail to support the idea that large portions of the molecular genetic results for vulnerability to substance dependence derive from factors that are limited to research volunteers. PMID:19094236
Fitzpatrick, Margaret A.; Hauser, Alan R.
Acinetobacter baumannii frequently causes nosocomial infections and outbreaks. Whole-genome sequencing (WGS) is a promising technique for strain typing and outbreak investigations. We compared the performance of conventional methods with WGS for strain typing clinical Acinetobacter isolates and analyzing a carbapenem-resistant A. baumannii (CRAB) outbreak. We performed two band-based typing techniques (pulsed-field gel electrophoresis and repetitive extragenic palindromic-PCR), multilocus sequence type (MLST) analysis, and WGS on 148 Acinetobacter calcoaceticus-A. baumannii complex bloodstream isolates collected from a single hospital from 2005 to 2012. Phylogenetic trees inferred from core-genome single nucleotide polymorphisms (SNPs) confirmed three Acinetobacter species within this collection. Four major A. baumannii clonal lineages (as defined by MLST) circulated during the study, three of which are globally distributed and one of which is novel. WGS indicated that a threshold of 2,500 core SNPs accurately distinguished A. baumannii isolates from different clonal lineages. The band-based techniques performed poorly in assigning isolates to clonal lineages and exhibited little agreement with sequence-based techniques. After applying WGS to a CRAB outbreak that occurred during the study, we identified a threshold of 2.5 core SNPs that distinguished nonoutbreak from outbreak strains. WGS was more discriminatory than the band-based techniques and was used to construct a more accurate transmission map that resolved many of the plausible transmission routes suggested by epidemiologic links. Our study demonstrates that WGS is superior to conventional techniques for A. baumannii strain typing and outbreak analysis. These findings support the incorporation of WGS into health care infection prevention efforts. PMID:26699703
Fitzpatrick, Margaret A; Ozer, Egon A; Hauser, Alan R
Acinetobacter baumannii frequently causes nosocomial infections and outbreaks. Whole-genome sequencing (WGS) is a promising technique for strain typing and outbreak investigations. We compared the performance of conventional methods with WGS for strain typing clinical Acinetobacter isolates and analyzing a carbapenem-resistant A. baumannii (CRAB) outbreak. We performed two band-based typing techniques (pulsed-field gel electrophoresis and repetitive extragenic palindromic-PCR), multilocus sequence type (MLST) analysis, and WGS on 148 Acinetobacter calcoaceticus-A. baumannii complex bloodstream isolates collected from a single hospital from 2005 to 2012. Phylogenetic trees inferred from core-genome single nucleotide polymorphisms (SNPs) confirmed three Acinetobacter species within this collection. Four major A. baumannii clonal lineages (as defined by MLST) circulated during the study, three of which are globally distributed and one of which is novel. WGS indicated that a threshold of 2,500 core SNPs accurately distinguished A. baumannii isolates from different clonal lineages. The band-based techniques performed poorly in assigning isolates to clonal lineages and exhibited little agreement with sequence-based techniques. After applying WGS to a CRAB outbreak that occurred during the study, we identified a threshold of 2.5 core SNPs that distinguished nonoutbreak from outbreak strains. WGS was more discriminatory than the band-based techniques and was used to construct a more accurate transmission map that resolved many of the plausible transmission routes suggested by epidemiologic links. Our study demonstrates that WGS is superior to conventional techniques for A. baumannii strain typing and outbreak analysis. These findings support the incorporation of WGS into health care infection prevention efforts.
Park, Si Nae; Huh, Sunghoon; Im, Kyongok; Choi, Sungbin; Chung, Hye Yoon; Huh, JooRyung; Seo, Eul-Ju; Lee, Je-Hwan; Bang, Duhee; Lee, Dong Soon
Chronic lymphocytic leukemia (CLL) is extremely rare in Asian countries and there has been one report on genetic changes for 5 genes (TP53, SF3B1, NOTCH1, MYD88, and BIRC3) by Sanger sequencing in Chinese CLL. Yet studies of CLL in Asian countries using Next generation sequencing have not been reported. We aimed to characterize the genomic profiles of Korean CLL and to find out ethnic differences in somatic mutations with prognostic implications. We performed targeted sequencing for 87 gene panel using next-generation sequencing along with G-banding and fluorescent in situ hybridization (FISH) for chromosome 12, 13q14.3 deletion, 17p13 deletion, and 11q22 deletion. Overall, 36 out of 48 patients (75%) harbored at least one mutation and mean number of mutation per patient was 1.6 (range 0–6). Aberrant karyotypes were observed in 30.4% by G-banding and 66.7% by FISH. Most recurrent mutation (>10% frequency) was ATM (20.8%) followed by TP53 (14.6%), SF3B1 (10.4%), KLHL6 (8.3%), and BCOR (6.25%). Mutations of MYD88 was associated with moderate adverse prognosis by multiple comparisons (P = 0.055). Mutation frequencies of MYD88, SAMHD1, EGR2, DDX3X, ZMYM3, and MED12 showed similar incidence with Caucasians, while mutation frequencies of ATM, TP53, KLHL6, BCOR and CDKN2A tend to be higher in Koreans than in Caucasians. Especially, ATM mutation showed 1.5 fold higher incidence than Caucasians, while mutation frequencies of SF3B1, NOTCH1, CHD2 and POT1 tend to be lower in Koreans than in Caucasians. However, mutation frequencies between Caucasians and Koreans were not significantly different statistically, probably due to low number of patients. Collectively, mutational profile and adverse prognostic genes in Korean CLL were different from those of Caucasians, suggesting an ethnic difference, while profile of cytogenetic aberrations was similar to those of Caucasians. PMID:27959900
Chokshi, Dave A.; Parker, Michael; Kwiatkowski, Dominic P.
Genomic epidemiology is a field of research that seeks to improve the prevention and management of common diseases through an understanding of their molecular origins. It involves studying thousands of individuals, often from different populations, with exacting techniques. The scale and complexity of such research has required the formation of research consortia. Members of these consortia need to agree on policies for managing shared resources and handling genetic data. Here we consider data-sharing and intellectual property policies for an international research consortium working on the genomic epidemiology of malaria. We outline specific guidelines governing how samples and data are transferred among its members; how results are released into the public domain; when to seek protection for intellectual property; and how intellectual property should be managed. We outline some pragmatic solutions founded on the basic principles of promoting innovation and access. PMID:16710548
Schabath, Matthew B.; Cress, W. Douglas; Muñoz-Antonia, Teresita
Background Globally and in the United States, lung cancer has been the most common cancer for the past several decades. In addition to the well-established geographical- and sex-specific differences in lung cancer incidence, mortality and survival, there is also growing evidence for racial and ethnic differences. Methods Based on available published data, we present a summary of the current knowledge and substantive findings related to racial and ethnic differences in lung cancer. Results Although this report is not a systematic review, we summarized the current knowledge and substantive findings related to racial and ethnic differences in lung cancer with a particular focus on lung cancer statistics(incidence, mortality, and survival), cigarette smoking, prevention and early detection, and the lung cancer genome. Finally, we summarize some the systems-level and provider-related issues that likely contribute to racial and ethnic-specific health disparities and provide some suggestions for future strategies that may reduce the disproportionate burden of lung cancer. Conclusions Although lung carcinogenesis is a multifactorial process driven by exogenous exposures (e.g., cigarette smoking), inherited genetic variations, and an accumulation of somatic genetic events, this multifactorial process appears to have racial and ethnic differences which in turn impacts the observed epidemiologic differences in incidence, mortality, and survival. PMID:27842323
Fjukstad, Bjørn; Standahl Olsen, Karina; Jareid, Mie; Lund, Eiliv; Bongo, Lars Ailo
Kvik is an open-source framework that we developed for explorative analysis of functional genomics data from large epidemiological studies. Creating such studies requires a significant amount of time and resources. It is therefore usual to reuse the data from one study for several research projects. Often each project requires implementing new analysis code, integration with specific knowledge bases, and specific visualizations. Although existing data exploration tools are available for single study data exploration, no tool provides all the required functionality for multistudy data exploration. We have therefore used the Kvik framework to develop Kvik Pathways, an application for exploring gene expression data in the context of biological pathways. We have used Kvik Pathways to explore data from both a cross-sectional study design and a case-control study within the Norwegian Women and Cancer (NOWAC) cohort. Kvik Pathways follows the three-tier architecture in web applications using a powerful back-end for statistical analyses and retrieval of metadata.In this note, we describe how we used the Kvik framework to develop the Kvik Pathways application. Kvik Pathways was used by our team of epidemiologists toexplore gene expression data from healthy women with high and low plasma ratios of essential fatty acids. PMID:26425340
Grad, Yonatan H; Waldor, Matthew K
The devastating Haitian cholera outbreak that began in October 2010 is the first known cholera epidemic in this island nation. Epidemiological and genomic data have provided strong evidence that United Nations security forces from Nepal introduced toxigenic Vibrio cholerae O1, the cause of epidemic cholera, to Haiti shortly before the outbreak arose. However, some have contended that indigenous V. cholerae contributed to the outbreak. In a recent paper (mBio 4:e00398-13, 2013), L. S. Katz et al. explored the nature and rate of changes in this ancient pathogen's genome during an outbreak, based on whole-genome sequencing of 23 Haitian V. cholerae clinical isolates obtained over a 20-month period. Notably, they detected point mutations, deletions, and inversions but found no insertion of horizontally transmitted DNA, arguing strongly against the idea that autochthonous V. cholerae donated DNA to the outbreak strain. Furthermore, they found that Haitian epidemic V. cholerae isolates were virtually untransformable. Comparative genomic analyses revealed that the Haitian isolates were nearly identical to isolates from Nepal and that the Nepalese-Haitian isolates were distinguishable from isolates circulating elsewhere in the world. Reconstruction of the phylogeny of the Haitian isolates was consistent with a single introduction of V. cholerae to Haiti sometime between late July and late October 2010, dates remarkably concordant with epidemiological observations. In aggregate, this paper provides additional compelling evidence that the V. cholerae strain responsible for the Haitian cholera epidemic came from Nepal and illustrates the power of whole-genome-based analyses for epidemiology, pathogen evolution, and forensics.
Kim, Ha-Hyun; Matthijnssens, Jelle; Kim, Hyun-Jeong; Kwon, Hyung-Jun; Park, Jun-Gyu; Son, Kyu-Yeol; Ryu, Eun-Hye; Kim, Deok-Song; Lee, Woo Song; Kang, Mun-Il; Yang, Dong-Kun; Hyun, Bang-Hun; Park, Sang-Ik; Park, Su-Jin; Cho, Kyoung-Oh
Group A rotaviruses (RVAs) are agents causing severe gastroenteritis in infants and young animals. G9 RVA strains are believed to have originated from pigs. However, this genotype has emerged as the fifth major human RVA genotype worldwide. To better understand the relationship between human and porcine RVA strains, complete RVA genome data are needed. For human RVA strains, the number of complete genome data have grown exponentially. However, there is still a lack of complete genome data on porcine RVA strains. Recently, G9 RVA strains have been identified as the third most important genotype in diarrheic pigs in South Korea in combinations with P and P. This study is the first report on complete genome analyses of 1 G9P and 3 G9P porcine RVA strains, resulting in the following genotype constellation: G9-P/P-I5-R1-C1-M1-A8-N1-T1-E1-H1. By comparisons of these genotype constellations, it was revealed that the Korean G9P and G9P RVA strains possessed a typical porcine RVA backbone, similar to other known porcine RVA strains. However, detailed phylogenetic analyses revealed the presence of intra-genotype reassortments among porcine RVA strains in South Korea. Thus, our data provide genetic information of G9 RVA strains increasingly detected in both humans and pigs, and will help to establish the role of pigs as a source or reservoir for novel human RVA strains.
Johnson, James R; Johnston, Brian; Kuskowski, Michael A; Nougayrede, Jean-Philippe; Oswald, Eric
Epidemiological and phylogenetic associations of the pks genomic island of extraintestinal pathogenic Escherichia coli (ExPEC), which encodes the genotoxin colibactin, are incompletely defined. clbB and clbN (as markers for the 5' and 3' regions of the pks island, respectively), clbA and clbQ (as supplemental pks island markers), and 12 other putative ExPEC virulence genes were newly sought by PCR among 131 published E. coli isolates from hospitalized veterans (62 blood isolates and 69 fecal isolates). Blood and fecal isolates and clbB-positive and -negative isolates were compared for 66 newly and previously assessed traits. Among the 14 newly sought traits, clbB and clbN (colibactin polyketide synthesis system), hra (heat-resistant agglutinin), and vat (vacuolating toxin) were significantly associated with bacteremia. clbB and clbN identified a subset within phylogenetic group B2 with extremely high virulence scores and a high proportion of blood isolates. However, by multivariable analysis, other traits were more predictive of blood source than clbB and clbN were; indeed, among the newly sought traits, only pic significantly predicted bacteremia (negative association). By correspondence analysis, clbB and clbN were closely associated with group B2 and multiple B2-associated traits; by principal coordinate analysis, clbB and clbN partitioned the data set better than did blood versus fecal source. Thus, the pks island was significantly associated with bacteremia, multiple ExPEC-associated virulence genes, and group B2, and within group B2, it identified an especially high-virulence subset. This extends previous work regarding the pks island and supports investigation of the colibactin system as a potential therapeutic target.
Marsh, Jane W.; Krauland, Mary G.; Nelson, Jemma S.; Schlackman, Jessica L.; Brooks, Anthony M.; Pasculle, A. William; Shutt, Kathleen A.; Doi, Yohei; Querry, Ashley M.; Muto, Carlene A.; Harrison, Lee H.
Increased incidence of infections due to Klebsiella pneumoniae carbapenemase (KPC)-producing Klebsiella pneumoniae (KPC-Kp) was noted among patients undergoing endoscopic retrograde cholangiopancreatography (ERCP) at a single hospital. An epidemiologic investigation identified KPC-Kp and non-KPC-producing, extended-spectrum β-lactamase (ESBL)-producing Kp in cultures from 2 endoscopes. Genotyping was performed on patient and endoscope isolates to characterize the microbial genomics of the outbreak. Genetic similarity of 51 Kp isolates from 37 patients and 3 endoscopes was assessed by pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST). Five patient and 2 endoscope isolates underwent whole genome sequencing (WGS). Two KPC-encoding plasmids were characterized by single molecule, real-time sequencing. Plasmid diversity was assessed by endonuclease digestion. Genomic and epidemiologic data were used in conjunction to investigate the outbreak source. Two clusters of Kp patient isolates were genetically related to endoscope isolates by PFGE. A subset of patient isolates were collected post-ERCP, suggesting ERCP endoscopes as a possible source. A phylogeny of 7 Kp genomes from patient and endoscope isolates supported ERCP as a potential source of transmission. Differences in gene content defined 5 ST258 subclades and identified 2 of the subclades as outbreak-associated. A novel KPC-encoding plasmid, pKp28 helped define and track one endoscope-associated ST258 subclade. WGS demonstrated high genetic relatedness of patient and ERCP endoscope isolates suggesting ERCP-associated transmission of ST258 KPC-Kp. Gene and plasmid content discriminated the outbreak from endemic ST258 populations and assisted with the molecular epidemiologic investigation of an extended KPC-Kp outbreak. PMID:26637170
Marsh, Jane W; Krauland, Mary G; Nelson, Jemma S; Schlackman, Jessica L; Brooks, Anthony M; Pasculle, A William; Shutt, Kathleen A; Doi, Yohei; Querry, Ashley M; Muto, Carlene A; Harrison, Lee H
Increased incidence of infections due to Klebsiella pneumoniae carbapenemase (KPC)-producing Klebsiella pneumoniae (KPC-Kp) was noted among patients undergoing endoscopic retrograde cholangiopancreatography (ERCP) at a single hospital. An epidemiologic investigation identified KPC-Kp and non-KPC-producing, extended-spectrum β-lactamase (ESBL)-producing Kp in cultures from 2 endoscopes. Genotyping was performed on patient and endoscope isolates to characterize the microbial genomics of the outbreak. Genetic similarity of 51 Kp isolates from 37 patients and 3 endoscopes was assessed by pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST). Five patient and 2 endoscope isolates underwent whole genome sequencing (WGS). Two KPC-encoding plasmids were characterized by single molecule, real-time sequencing. Plasmid diversity was assessed by endonuclease digestion. Genomic and epidemiologic data were used in conjunction to investigate the outbreak source. Two clusters of Kp patient isolates were genetically related to endoscope isolates by PFGE. A subset of patient isolates were collected post-ERCP, suggesting ERCP endoscopes as a possible source. A phylogeny of 7 Kp genomes from patient and endoscope isolates supported ERCP as a potential source of transmission. Differences in gene content defined 5 ST258 subclades and identified 2 of the subclades as outbreak-associated. A novel KPC-encoding plasmid, pKp28 helped define and track one endoscope-associated ST258 subclade. WGS demonstrated high genetic relatedness of patient and ERCP endoscope isolates suggesting ERCP-associated transmission of ST258 KPC-Kp. Gene and plasmid content discriminated the outbreak from endemic ST258 populations and assisted with the molecular epidemiologic investigation of an extended KPC-Kp outbreak.
Orlek, Alex; Stoesser, Nicole; Anjum, Muna F; Doumith, Michel; Ellington, Matthew J; Peto, Tim; Crook, Derrick; Woodford, Neil; Walker, A Sarah; Phan, Hang; Sheppard, Anna E
Plasmids are extra-chromosomal genetic elements ubiquitous in bacteria, and commonly transmissible between host cells. Their genomes include variable repertoires of 'accessory genes,' such as antibiotic resistance genes, as well as 'backbone' loci which are largely conserved within plasmid families, and often involved in key plasmid-specific functions (e.g., replication, stable inheritance, mobility). Classifying plasmids into different types according to their phylogenetic relatedness provides insight into the epidemiology of plasmid-mediated antibiotic resistance. Current typing schemes exploit backbone loci associated with replication (replicon typing), or plasmid mobility (MOB typing). Conventional PCR-based methods for plasmid typing remain widely used. With the emergence of whole-genome sequencing (WGS), large datasets can be analyzed using in silico plasmid typing methods. However, short reads from popular high-throughput sequencers can be challenging to assemble, so complete plasmid sequences may not be accurately reconstructed. Therefore, localizing resistance genes to specific plasmids may be difficult, limiting epidemiological insight. Long-read sequencing will become increasingly popular as costs decline, especially when resolving accurate plasmid structures is the primary goal. This review discusses the application of plasmid classification in WGS-based studies of antibiotic resistance epidemiology; novel in silico plasmid analysis tools are highlighted. Due to the diverse and plastic nature of plasmid genomes, current typing schemes do not classify all plasmids, and identifying conserved, phylogenetically concordant genes for subtyping and phylogenetics is challenging. Analyzing plasmids as nodes in a network that represents gene-sharing relationships between plasmids provides a complementary way to assess plasmid diversity, and allows inferences about horizontal gene transfer to be made.
Orlek, Alex; Stoesser, Nicole; Anjum, Muna F.; Doumith, Michel; Ellington, Matthew J.; Peto, Tim; Crook, Derrick; Woodford, Neil; Walker, A. Sarah; Phan, Hang; Sheppard, Anna E.
Plasmids are extra-chromosomal genetic elements ubiquitous in bacteria, and commonly transmissible between host cells. Their genomes include variable repertoires of ‘accessory genes,’ such as antibiotic resistance genes, as well as ‘backbone’ loci which are largely conserved within plasmid families, and often involved in key plasmid-specific functions (e.g., replication, stable inheritance, mobility). Classifying plasmids into different types according to their phylogenetic relatedness provides insight into the epidemiology of plasmid-mediated antibiotic resistance. Current typing schemes exploit backbone loci associated with replication (replicon typing), or plasmid mobility (MOB typing). Conventional PCR-based methods for plasmid typing remain widely used. With the emergence of whole-genome sequencing (WGS), large datasets can be analyzed using in silico plasmid typing methods. However, short reads from popular high-throughput sequencers can be challenging to assemble, so complete plasmid sequences may not be accurately reconstructed. Therefore, localizing resistance genes to specific plasmids may be difficult, limiting epidemiological insight. Long-read sequencing will become increasingly popular as costs decline, especially when resolving accurate plasmid structures is the primary goal. This review discusses the application of plasmid classification in WGS-based studies of antibiotic resistance epidemiology; novel in silico plasmid analysis tools are highlighted. Due to the diverse and plastic nature of plasmid genomes, current typing schemes do not classify all plasmids, and identifying conserved, phylogenetically concordant genes for subtyping and phylogenetics is challenging. Analyzing plasmids as nodes in a network that represents gene-sharing relationships between plasmids provides a complementary way to assess plasmid diversity, and allows inferences about horizontal gene transfer to be made. PMID:28232822
Lee, Jong-Seung; Cho, Won Kyong; Kim, Mi-Kyeong; Kwak, Hae-Ryun; Choi, Hong-Soo; Kim, Kook-Hyung
Tomato spotted wilt virus (TSWV) infects numerous host plants and has three genome segments, called L, M and S. Here, we report the complete genome sequences of three Korean TSWV isolates (TSWV-1 to -3) infecting tomato and pepper plants. Although the nucleotide sequence of TSWV-1 genome isolated from tomato is very different from those of TSWV-2 and TSWV-3 isolated from pepper, the deduced amino acid sequences of the five TSWV genes are highly conserved among all three TSWV isolates. In phylogenetic analysis, deduced RdRp protein sequences of TSWV-2 and TSWV-3 were clustered together with two previously reported isolates from Japan and Korea, while TSWV-1 grouped together with a Hawaiian isolate. A phylogenetic tree based on N protein sequences, however, revealed four distinct groups of TSWV isolates, and all three Korean isolates belonged to group II, together with many other isolates, mostly from Europe and Asia. Interestingly, most American isolates grouped together as group I. Together, these results suggested that these newly identified TSWV isolates might have originated from an Asian ancestor and undergone divergence upon infecting different host plants.
The Republic of Korea occupies approximately 38,000 square miles in the southern position of a mountaineous peninsula. It shares a land boundary with North Korea. With a population of more than 40 million people, South Korea has 1 of the highest population densities in the world. The language spoken is a Uralic language, closely akin to Japanese, Hungarian, Finnish, and Mongolian, and the traditional religions are Shamanism and Buddhism. Over the course of time, South Korea has been invaded and fought over by its neighbors. The US and the Soviet Union have never been able to reach a unification agreement for North and South Korea. The 3rd Republic era, begun in 1963, saw a time of rapid industrialization and a great deal of economic growth. The 5th Republic began with a new constitution and new elections brought about the election of a president to a 7-year term of office beginning in 1981. Economic growth has been remarkable over the last 25 years despite the fact that North Korea possesses most of the mineral and hydroelectric resources and the existing heavy industrial base built by the Japanese while South Korea has the limited agricultural resources and had, initially, a large unskilled labor pool. Serious industrial growth began in South Korea in the early 1960s and the GNP grew at an annual rate of 10% during the period 1963-78. Current GNP is now, at $2000, well beyond that of its neighbors to the north. The outlook for longterm growth is good; however, the military threat posed by North Korea and the absence of foreign economic assistance has resulted in Korea spending 1/3 of its budget on defense. South Korea is active in international affairs and in the UN. Economic realities have forced Korea to give economics priority in their foreign policy. There has been an on-again, off-again quality to dialogue between the 2 nations. However, the US is committed to maintaining peace on the Korean peninsula. In order to do so, they have supplied manpower and
The Cancer Epidemiology Matters blog helps foster a dialogue between the National Cancer Institute's (NCI) Epidemiology and Genomics Research Program (EGRP), extramural researchers, and other individuals, such as clinicians, community partners, and advocates, who are interested in cancer epidemiology and genomics.
Demczuk, Walter; Martin, Irene; Peterson, Shelley; Bharat, Amrita; Van Domselaar, Gary; Graham, Morag; Lefebvre, Brigitte; Allen, Vanessa; Hoang, Linda; Tyrrell, Greg; Horsman, Greg; Wylie, John; Haldane, David; Archibald, Chris; Wong, Tom; Unemo, Magnus
The emergence of Neisseria gonorrhoeae strains with decreased susceptibility to cephalosporins and azithromycin (AZM) resistance (AZMr) represents a public health threat of untreatable gonorrhea infections. Genomic epidemiology through whole-genome sequencing was used to describe the emergence, dissemination, and spread of AZMr strains. The genomes of 213 AZMr and 23 AZM-susceptible N. gonorrhoeae isolates collected in Canada from 1989 to 2014 were sequenced. Core single nucleotide polymorphism (SNP) phylogenomic analysis resolved 246 isolates into 13 lineages. High-level AZMr (MICs ≥ 256 μg/ml) was found in 5 phylogenetically diverse isolates, all of which possessed the A2059G mutation (Escherichia coli numbering) in all four 23S rRNA alleles. One isolate with high-level AZMr collected in 2009 concurrently had decreased susceptibility to ceftriaxone (MIC = 0.125 μg/ml). An increase in the number of 23S rRNA alleles with the C2611T mutations (E. coli numbering) conferred low to moderate levels of AZMr (MICs = 2 to 4 and 8 to 32 μg/ml, respectively). Low-level AZMr was also associated with mtrR promoter mutations, including the −35A deletion and the presence of Neisseria meningitidis-like sequences. Geographic and temporal phylogenetic clustering indicates that emergent AZMr strains arise independently and can then rapidly expand clonally in a region through local sexual networks. PMID:26935729
Debette, Stéphanie; Ibrahim Verbaas, Carla A.; Bressler, Jan; Schuur, Maaike; Smith, Albert; Bis, Joshua C.; Davies, Gail; Wolf, Christiane; Gudnason, Vilmundur; Chibnik, Lori B.; Yang, Qiong; deStefano, Anita L.; de Quervain, Dominique J.F.; Srikanth, Velandai; Lahti, Jari; Grabe, Hans J.; Smith, Jennifer A.; Priebe, Lutz; Yu, Lei; Karbalai, Nazanin; Hayward, Caroline; Wilson, James F.; Campbell, Harry; Petrovic, Katja; Fornage, Myriam; Chauhan, Ganesh; Yeo, Robin; Boxall, Ruth; Becker, James; Stegle, Oliver; Mather, Karen A.; Chouraki, Vincent; Sun, Qi; Rose, Lynda M.; Resnick, Susan; Oldmeadow, Christopher; Kirin, Mirna; Wright, Alan F.; Jonsdottir, Maria K.; Au, Rhoda; Becker, Albert; Amin, Najaf; Nalls, Mike A.; Turner, Stephen T.; Kardia, Sharon L.R.; Oostra, Ben; Windham, Gwen; Coker, Laura H.; Zhao, Wei; Knopman, David S.; Heiss, Gerardo; Griswold, Michael E.; Gottesman, Rebecca F.; Vitart, Veronique; Hastie, Nicholas D.; Zgaga, Lina; Rudan, Igor; Polasek, Ozren; Holliday, Elizabeth G.; Schofield, Peter; Choi, Seung Hoan; Tanaka, Toshiko; An, Yang; Perry, Rodney T.; Kennedy, Richard E.; Sale, Michèle M.; Wang, Jing; Wadley, Virginia G.; Liewald, David C.; Ridker, Paul M.; Gow, Alan J.; Pattie, Alison; Starr, John M.; Porteous, David; Liu, Xuan; Thomson, Russell; Armstrong, Nicola J.; Eiriksdottir, Gudny; Assareh, Arezoo A.; Kochan, Nicole A.; Widen, Elisabeth; Palotie, Aarno; Hsieh, Yi-Chen; Eriksson, Johan G.; Vogler, Christian; van Swieten, John C.; Shulman, Joshua M.; Beiser, Alexa; Rotter, Jerome; Schmidt, Carsten O.; Hoffmann, Wolfgang; Nöthen, Markus M.; Ferrucci, Luigi; Attia, John; Uitterlinden, Andre G.; Amouyel, Philippe; Dartigues, Jean-François; Amieva, Hélène; Räikkönen, Katri; Garcia, Melissa; Wolf, Philip A.; Hofman, Albert; Longstreth, W.T.; Psaty, Bruce M.; Boerwinkle, Eric; DeJager, Philip L.; Sachdev, Perminder S.; Schmidt, Reinhold; Breteler, Monique M.B.; Teumer, Alexander; Lopez, Oscar L.; Cichon, Sven; Chasman, Daniel I.; Grodstein, Francine; Müller-Myhsok, Bertram; Tzourio, Christophe; Papassotiropoulos, Andreas; Bennett, David A.; Ikram, Arfan M.; Deary, Ian J.; van Duijn, Cornelia M.; Launer, Lenore; Fitzpatrick, Annette L.; Seshadri, Sudha; Mosley, Thomas H.
BACKGROUND Memory performance in older persons can reflect genetic influences on cognitive function and dementing processes. We aimed to identify genetic contributions to verbal declarative memory in a community setting. METHODS We conducted genome-wide association studies for paragraph or word list delayed recall in 19 cohorts from the Cohorts for Heart and Aging Research in Genomic Epidemiology consortium, comprising 29,076 dementia-and stroke-free individuals of European descent, aged ≥45 years. Replication of suggestive associations (p < 5 × 10−6) was sought in 10,617 participants of European descent, 3811 African-Americans, and 1561 young adults. RESULTS rs4420638, near APOE, was associated with poorer delayed recall performance in discovery (p = 5.57 × 10−10) and replication cohorts (p = 5.65 × 10−8). This association was stronger for paragraph than word list delayed recall and in the oldest persons. Two associations with specific tests, in subsets of the total sample, reached genome-wide significance in combined analyses of discovery and replication (rs11074779 [HS3ST4], p = 3.11 × 10−8, and rs6813517 [SPOCK3], p = 2.58 × 10−8) near genes involved in immune response. A genetic score combining 58 independent suggestive memory risk variants was associated with increasing Alzheimer disease pathology in 725 autopsy samples. Association of memory risk loci with gene expression in 138 human hippocampus samples showed cis-associations with WDR48 and CLDN5, both related to ubiquitin metabolism. CONCLUSIONS This largest study to date exploring the genetics of memory function in ~ 40,000 older individuals revealed genome-wide associations and suggested an involvement of immune and ubiquitin pathways. PMID:25648963
Roy, Deodutta; Morgan, Marisa; Yoo, Changwon; Deoraj, Alok; Roy, Sandhya; Yadav, Vijay Kumar; Garoub, Mohannad; Assaggaf, Hamza; Doke, Mayur
We present a combined environmental epidemiologic, genomic, and bioinformatics approach to identify: exposure of environmental chemicals with estrogenic activity; epidemiologic association between endocrine disrupting chemical (EDC) and health effects, such as, breast cancer or endometriosis; and gene-EDC interactions and disease associations. Human exposure measurement and modeling confirmed estrogenic activity of three selected class of environmental chemicals, polychlorinated biphenyls (PCBs), bisphenols (BPs), and phthalates. Meta-analysis showed that PCBs exposure, not Bisphenol A (BPA) and phthalates, increased the summary odds ratio for breast cancer and endometriosis. Bioinformatics analysis of gene-EDC interactions and disease associations identified several hundred genes that were altered by exposure to PCBs, phthalate or BPA. EDCs-modified genes in breast neoplasms and endometriosis are part of steroid hormone signaling and inflammation pathways. All three EDCs–PCB 153, phthalates, and BPA influenced five common genes—CYP19A1, EGFR, ESR2, FOS, and IGF1—in breast cancer as well as in endometriosis. These genes are environmentally and estrogen responsive, altered in human breast and uterine tumors and endometriosis lesions, and part of Mitogen Activated Protein Kinase (MAPK) signaling pathways in cancer. Our findings suggest that breast cancer and endometriosis share some common environmental and molecular risk factors. PMID:26512648
Baltrus, David A; McCann, Honour C; Guttman, David S
A remarkable shift in our understanding of plant-pathogenic bacteria is underway. Until recently, nearly all research on phytopathogenic bacteria was focused on a small number of model strains, which provided a deep, but narrow, perspective on plant-microbe interactions. Advances in genome sequencing technologies have changed this by enabling the incorporation of much greater diversity into comparative and functional research. We are now moving beyond a typological understanding of a select collection of strains to a more generalized appreciation of the breadth and scope of plant-microbe interactions. The study of natural populations and evolution has particularly benefited from the expansion of genomic data. We are beginning to have a much deeper understanding of the natural genetic diversity, niche breadth, ecological constraints and defining characteristics of phytopathogenic species. Given this expanding genomic and ecological knowledge, we believe the time is ripe to evaluate what we know about the evolutionary dynamics of plant pathogens.
Legrottaglie, R; Rizzi, V; Agrimi, P
Fifteen bovine rotavirus group A strains were isolated in several Italian regions over the period 1981-1989 from calves in ten neonatal diarrhoea outbreaks. The electrophoretical analysis of the genoma showed genomic variations and five different profiles were observed, including one with thirteen dsRNA segments. The finding of extra RNA fragments, with respect to the regular eleven genome segments, suggests the possibility of simultaneous or sequential infection by more than one electropherotype or a modification in the length of RNA segments during infection.
Salmonella enterica serotype Enteritidis (SE) is one of the most commonly reported causes of human salmonellosis. The low genetic diversity of SE measured by fingerprinting methods has made subtyping a challenge. In this study, we used whole genome sequencing to characterize a total of 125 SE and Sa...
Ou, Hong-Yu; Kuang, Shan N.; He, Xinyi; Molgora, Brenda M.; Ewing, Peter J.; Deng, Zixin; Osby, Melanie; Chen, Wangxue; Xu, H. Howard
Acinetobacter baumannii is an important human pathogen due to its multi-drug resistance. In this study, the genome of an ST10 outbreak A. baumannii isolate LAC-4 was completely sequenced to better understand its epidemiology, antibiotic resistance genetic determinants and potential virulence factors. Compared with 20 other complete genomes of A. baumannii, LAC-4 genome harbors at least 12 copies of five distinct insertion sequences. It contains 12 and 14 copies of two novel IS elements, ISAba25 and ISAba26, respectively. Additionally, three novel composite transposons were identified: Tn6250, Tn6251 and Tn6252, two of which contain resistance genes. The antibiotic resistance genetic determinants on the LAC-4 genome correlate well with observed antimicrobial susceptibility patterns. Moreover, twelve genomic islands (GI) were identified in LAC-4 genome. Among them, the 33.4-kb GI12 contains a large number of genes which constitute the K (capsule) locus. LAC-4 harbors several unique putative virulence factor loci. Furthermore, LAC-4 and all 19 other outbreak isolates were found to harbor a heme oxygenase gene (hemO)-containing gene cluster. The sequencing of the first complete genome of an ST10 A. baumannii clinical strain should accelerate our understanding of the epidemiology, mechanisms of resistance and virulence of A. baumannii. PMID:25728466
McCallum, Nadine; Gray, Timothy J; Wang, Qinning; Ng, Jimmy; Hicks, Leanne; Nguyen, Trang; Yuen, Marion; Hill-Cawthorne, Grant A; Sintchenko, Vitali
Infant botulism is a potentially life-threatening paralytic disease that can be associated with prolonged morbidity if not rapidly diagnosed and treated. Four infants were diagnosed and treated for infant botulism in NSW, Australia, between May 2011 and August 2013. Despite the temporal relationship between the cases, there was no close geographical clustering or other epidemiological links. Clostridium botulinum isolates, three of which produced botulism neurotoxin serotype A (BoNT/A) and one BoNT serotype B (BoNT/B), were characterized using whole-genome sequencing (WGS). In silico multilocus sequence typing (MLST) found that two of the BoNT/A-producing isolates shared an identical novel sequence type, ST84. The other two isolates were single-locus variants of this sequence type (ST85 and ST86). All BoNT/A-producing isolates contained the same chromosomally integrated BoNT/A2 neurotoxin gene cluster. The BoNT/B-producing isolate carried a single plasmid-borne bont/B gene cluster, encoding BoNT subtype B6. Single nucleotide polymorphism (SNP)-based typing results corresponded well with MLST; however, the extra resolution provided by the whole-genome SNP comparisons showed that the isolates differed from each other by >3,500 SNPs. WGS analyses indicated that the four infant botulism cases were caused by genomically distinct strains of C. botulinum that were unlikely to have originated from a common environmental source. The isolates did, however, cluster together, compared with international isolates, suggesting that C. botulinum from environmental reservoirs throughout NSW have descended from a common ancestor. Analyses showed that the high resolution of WGS provided important phylogenetic information that would not be captured by standard seven-loci MLST.
Shah, Muhammad Ali; Mutreja, Ankur; Thomson, Nicholas; Baker, Stephen; Parkhill, Julian; Dougan, Gordon; Bokhari, Habib; Wren, Brendan W
In August 2010, Pakistan experienced major floods and a subsequent cholera epidemic. To clarify the population dynamics and transmission of Vibrio cholerae in Pakistan, we sequenced the genomes of all V. cholerae O1 El Tor isolates and compared the sequences to a global collection of 146 V. cholerae strains. Within the global phylogeny, all isolates from Pakistan formed 2 new subclades (PSC-1 and PSC-2), lying in the third transmission wave of the seventh-pandemic lineage that could be distinguished by signature deletions and their antimicrobial susceptibilities. Geographically, PSC-1 isolates originated from the coast, whereas PSC-2 isolates originated from inland areas flooded by the Indus River. Single-nucleotide polymorphism accumulation analysis correlated river flow direction with the spread of PSC-2. We found at least 2 sources of cholera in Pakistan during the 2010 epidemic and illustrate the value of a global genomic data bank in contextualizing cholera outbreaks.
Caddy, Sarah L; Goodfellow, Ian
Astroviruses are a common cause of gastroenteritis in children worldwide. These viruses can also cause infection in a range of domestic and wild animal species. Canine astrovirus (CaAstV) was first identified in the USA, and has since been reported in dogs from Europe, the Far East and South America. We sought to determine whether CaAstV is circulating in the UK dog population, and to characterise any identified strains. Stool samples were collected from pet dogs in the UK with and without gastroenteritis, and samples were screened for CaAstV by qPCR. Four CaAstV positive samples were identified from dogs with gastroenteritis (4/67, 6.0%), whereas no samples from healthy dogs were positive (p<0.001). Sequencing of the capsid sequences from the four CaAstV strains found significant genetic heterogeneity, with only 80% amino acid identity between strains. The full genome sequence of two UK CaAstV strains was then determined, confirming that CaAstV conforms to the classic genome organisation of other astroviruses with ORF1a and ORF1b separated by a frameshift and ORF2 encoding the capsid protein. This is the first report describing the circulation of CaAstV in UK dogs with clinical signs of gastroenteritis, and the first description of the full-length genomes of two CaAstV strains.
EPIDEMIOLOGY, *TYPHOID, SENSITIVITY, MEDIA, PUBLIC HEALTH, CULTURES(BIOLOGY), SOUTH KOREA, SHIGELLA, ANTIBIOTICS , RESISTANCE (BIOLOGY), BLOOD ANALYSIS, FOOD HANDLERS, SALMONELLA PARATYPHI, SALMONELLA TYPHIMURIUM.
Mentasti, Massimo; Tewolde, Rediat; Aslett, Martin; Harris, Simon R.; Afshar, Baharak; Underwood, Anthony; Harrison, Timothy G.
Sequence-based typing (SBT), analogous to multilocus sequence typing (MLST), is the current “gold standard” typing method for investigation of legionellosis outbreaks caused by Legionella pneumophila. However, as common sequence types (STs) cause many infections, some investigations remain unresolved. In this study, various whole-genome sequencing (WGS)-based methods were evaluated according to published guidelines, including (i) a single nucleotide polymorphism (SNP)-based method, (ii) extended MLST using different numbers of genes, (iii) determination of gene presence or absence, and (iv) a kmer-based method. L. pneumophila serogroup 1 isolates (n = 106) from the standard “typing panel,” previously used by the European Society for Clinical Microbiology Study Group on Legionella Infections (ESGLI), were tested together with another 229 isolates. Over 98% of isolates were considered typeable using the SNP- and kmer-based methods. Percentages of isolates with complete extended MLST profiles ranged from 99.1% (50 genes) to 86.8% (1,455 genes), while only 41.5% produced a full profile with the gene presence/absence scheme. Replicates demonstrated that all methods offer 100% reproducibility. Indices of discrimination range from 0.972 (ribosomal MLST) to 0.999 (SNP based), and all values were higher than that achieved with SBT (0.940). Epidemiological concordance is generally inversely related to discriminatory power. We propose that an extended MLST scheme with ∼50 genes provides optimal epidemiological concordance while substantially improving the discrimination offered by SBT and can be used as part of a hierarchical typing scheme that should maintain backwards compatibility and increase discrimination where necessary. This analysis will be useful for the ESGLI to design a scheme that has the potential to become the new gold standard typing method for L. pneumophila. PMID:27280420
Li, Changwei; He, Jiang; Chen, Jing; Zhao, Jinying; Gu, Dongfeng; Hixson, James E; Rao, Dabeeru C; Jaquish, Cashell E; Gu, Charles C; Chen, Jichun; Huang, Jianfeng; Chen, Shufeng; Kelly, Tanika N
We performed genome-wide analyses to identify genomic loci that interact with sodium to influence blood pressure (BP) using single-marker-based (1 and 2 df joint tests) and gene-based tests among 1876 Chinese participants of the Genetic Epidemiology Network of Salt-Sensitivity (GenSalt) study. Among GenSalt participants, the average of 3 urine samples was used to estimate sodium excretion. Nine BP measurements were taken using a random zero sphygmomanometer. A total of 2.05 million single-nucleotide polymorphisms were imputed using Affymetrix 6.0 genotype data and the Chinese Han of Beijing and Japanese of Tokyo HapMap reference panel. Promising findings (P<1.00×10(-4)) from GenSalt were evaluated for replication among 775 Chinese participants of the Multi-Ethnic Study of Atherosclerosis (MESA). Single-nucleotide polymorphism and gene-based results were meta-analyzed across the GenSalt and MESA studies to determine genome-wide significance. The 1 df tests identified interactions for UST rs13211840 on diastolic BP (P=3.13×10(-9)). The 2 df tests additionally identified associations for CLGN rs2567241 (P=3.90×10(-12)) and LOC105369882 rs11104632 (P=4.51×10(-8)) with systolic BP. The CLGN variant rs2567241 was also associated with diastolic BP (P=3.11×10(-22)) and mean arterial pressure (P=2.86×10(-15)). Genome-wide gene-based analysis identified MKNK1 (P=6.70×10(-7)), C2orf80 (P<1.00×10(-12)), EPHA6 (P=2.88×10(-7)), SCOC-AS1 (P=4.35×10(-14)), SCOC (P=6.46×10(-11)), CLGN (P=3.68×10(-13)), MGAT4D (P=4.73×10(-11)), ARHGAP42 (P≤1.00×10(-12)), CASP4 (P=1.31×10(-8)), and LINC01478 (P=6.75×10(-10)) that were associated with at least 1 BP phenotype. In summary, we identified 8 novel and 1 previously reported BP loci through the examination of single-nucleotide polymorphism and gene-based interactions with sodium.
Background Although smoking behavior is known to affect body mass index (BMI), the potential for smoking to influence genetic associations with BMI is largely unexplored. Methods As part of the ‘Population Architecture using Genomics and Epidemiology (PAGE)’ Consortium, we investigated interaction between genetic risk factors associated with BMI and smoking for 10 single nucleotide polymorphisms (SNPs) previously identified in genome-wide association studies. We included 6 studies with a total of 56,466 subjects (16,750 African Americans (AA) and 39,716 European Americans (EA)). We assessed effect modification by testing an interaction term for each SNP and smoking (current vs. former/never) in the linear regression and by stratified analyses. Results We did not observe strong evidence for interactions and only observed two interactions with p-values <0.1: for rs6548238/TMEM18, the risk allele (C) was associated with BMI only among AA females who were former/never smokers (β = 0.018, p = 0.002), vs. current smokers (β = 0.001, p = 0.95, pinteraction = 0.10). For rs9939609/FTO, the A allele was more strongly associated with BMI among current smoker EA females (β = 0.017, p = 3.5x10-5), vs. former/never smokers (β = 0.006, p = 0.05, pinteraction = 0.08). Conclusions These analyses provide limited evidence that smoking status may modify genetic effects of previously identified genetic risk factors for BMI. Larger studies are needed to follow up our results. Clinical Trial Registration NCT00000611 PMID:23311614
Dumitrescu, Logan; Carty, Cara L; Taylor, Kira; Schumacher, Fredrick R; Hindorff, Lucia A; Ambite, José L; Anderson, Garnet; Best, Lyle G; Brown-Gentry, Kristin; Bůžková, Petra; Carlson, Christopher S; Cochran, Barbara; Cole, Shelley A; Devereux, Richard B; Duggan, Dave; Eaton, Charles B; Fornage, Myriam; Franceschini, Nora; Haessler, Jeff; Howard, Barbara V; Johnson, Karen C; Laston, Sandra; Kolonel, Laurence N; Lee, Elisa T; MacCluer, Jean W; Manolio, Teri A; Pendergrass, Sarah A; Quibrera, Miguel; Shohet, Ralph V; Wilkens, Lynne R; Haiman, Christopher A; Le Marchand, Loïc; Buyske, Steven; Kooperberg, Charles; North, Kari E; Crawford, Dana C
For the past five years, genome-wide association studies (GWAS) have identified hundreds of common variants associated with human diseases and traits, including high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), and triglyceride (TG) levels. Approximately 95 loci associated with lipid levels have been identified primarily among populations of European ancestry. The Population Architecture using Genomics and Epidemiology (PAGE) study was established in 2008 to characterize GWAS-identified variants in diverse population-based studies. We genotyped 49 GWAS-identified SNPs associated with one or more lipid traits in at least two PAGE studies and across six racial/ethnic groups. We performed a meta-analysis testing for SNP associations with fasting HDL-C, LDL-C, and ln(TG) levels in self-identified European American (~20,000), African American (~9,000), American Indian (~6,000), Mexican American/Hispanic (~2,500), Japanese/East Asian (~690), and Pacific Islander/Native Hawaiian (~175) adults, regardless of lipid-lowering medication use. We replicated 55 of 60 (92%) SNP associations tested in European Americans at p<0.05. Despite sufficient power, we were unable to replicate ABCA1 rs4149268 and rs1883025, CETP rs1864163, and TTC39B rs471364 previously associated with HDL-C and MAFB rs6102059 previously associated with LDL-C. Based on significance (p<0.05) and consistent direction of effect, a majority of replicated genotype-phentoype associations for HDL-C, LDL-C, and ln(TG) in European Americans generalized to African Americans (48%, 61%, and 57%), American Indians (45%, 64%, and 77%), and Mexican Americans/Hispanics (57%, 56%, and 86%). Overall, 16 associations generalized across all three populations. For the associations that did not generalize, differences in effect sizes, allele frequencies, and linkage disequilibrium offer clues to the next generation of association studies for these traits.
Andam, Cheryl P; Mitchell, Patrick K; Callendrello, Alanna; Chang, Qiuzhi; Corander, Jukka; Chaguza, Chrispin; McGee, Lesley; Beall, Bernard W; Hanage, William P
Conjugate vaccination against seven pneumococcal serotypes (PCV7) reduced disease prevalence due to antibiotic-resistant strains throughout the 2000s. However, diseases caused by resistant nonvaccine type (NVT) strains increased. Some of these emerging strains were derived from vaccine types (VT) that had changed their capsule by recombination. The introduction of a vaccine targeting 13 serotypes (PCV13) in 2010 has led to concern that this scenario will repeat itself. We generated high-quality draft genomes from 265 isolates of NVT pneumococci not susceptible to penicillin (PNSP) in 2009 and compared them with the genomes of 581 isolates from 2012 to 2013 collected by the Active Bacterial Core surveillance (ABCs) of the Centers for Disease Control and Prevention (CDC). Of the seven sequence clusters (SCs) identified, three SCs fell into a single lineage associated with serogroup 23, which had an origin in 1908 as dated by coalescent analysis and included isolates with a divergent 23B capsule locus. Three other SCs represented relatively deep-branching lineages associated with serotypes 35B, 15A, and 15BC. In all cases, the resistant clones originated prior to 2010, indicating that PNSP are at present dominated by descendants of NVT clones present before vaccination. With one exception (15BC/ST3280), these SCs were related to clones identified by the Pneumococcal Molecular Epidemiology Network (PMEN). We conclude that postvaccine diversity in NVT PNSP between 2009 and 2013 was driven mainly by the persistence of preexisting strains rather than through de novo adaptation, with few cases of serotype switching. Future surveillance is essential for documenting the long-term dynamics and resistance of NVT PNSP.
Forde, Taya L; Orsel, Karin; Zadoks, Ruth N; Biek, Roman; Adams, Layne G; Checkley, Sylvia L; Davison, Tracy; De Buck, Jeroen; Dumond, Mathieu; Elkin, Brett T; Finnegan, Laura; Macbeth, Bryan J; Nelson, Cait; Niptanatiak, Amanda; Sather, Shane; Schwantje, Helen M; van der Meer, Frank; Kutz, Susan J
Northern ecosystems are currently experiencing unprecedented ecological change, largely driven by a rapidly changing climate. Pathogen range expansion, and emergence and altered patterns of infectious disease, are increasingly reported in wildlife at high latitudes. Understanding the causes and consequences of shifting pathogen diversity and host-pathogen interactions in these ecosystems is important for wildlife conservation, and for indigenous populations that depend on wildlife. Among the key questions are whether disease events are associated with endemic or recently introduced pathogens, and whether emerging strains are spreading throughout the region. In this study, we used a phylogenomic approach to address these questions of pathogen endemicity and spread for Erysipelothrix rhusiopathiae, an opportunistic multi-host bacterial pathogen associated with recent mortalities in arctic and boreal ungulate populations in North America. We isolated E. rhusiopathiae from carcasses associated with large-scale die-offs of muskoxen in the Canadian Arctic Archipelago, and from contemporaneous mortality events and/or population declines among muskoxen in northwestern Alaska and caribou and moose in western Canada. Bacterial genomic diversity differed markedly among these locations; minimal divergence was present among isolates from muskoxen in the Canadian Arctic, while in caribou and moose populations, strains from highly divergent clades were isolated from the same location, or even from within a single carcass. These results indicate that mortalities among northern ungulates are not associated with a single emerging strain of E. rhusiopathiae, and that alternate hypotheses need to be explored. Our study illustrates the value and limitations of bacterial genomic data for discriminating between ecological hypotheses of disease emergence, and highlights the importance of studying emerging pathogens within the broader context of environmental and host factors.
Forde, Taya L.; Orsel, Karin; Zadoks, Ruth N.; Biek, Roman; Adams, Layne G.; Checkley, Sylvia L.; Davison, Tracy; De Buck, Jeroen; Dumond, Mathieu; Elkin, Brett T.; Finnegan, Laura; Macbeth, Bryan J.; Nelson, Cait; Niptanatiak, Amanda; Sather, Shane; Schwantje, Helen M.; van der Meer, Frank; Kutz, Susan J.
Northern ecosystems are currently experiencing unprecedented ecological change, largely driven by a rapidly changing climate. Pathogen range expansion, and emergence and altered patterns of infectious disease, are increasingly reported in wildlife at high latitudes. Understanding the causes and consequences of shifting pathogen diversity and host-pathogen interactions in these ecosystems is important for wildlife conservation, and for indigenous populations that depend on wildlife. Among the key questions are whether disease events are associated with endemic or recently introduced pathogens, and whether emerging strains are spreading throughout the region. In this study, we used a phylogenomic approach to address these questions of pathogen endemicity and spread for Erysipelothrix rhusiopathiae, an opportunistic multi-host bacterial pathogen associated with recent mortalities in arctic and boreal ungulate populations in North America. We isolated E. rhusiopathiae from carcasses associated with large-scale die-offs of muskoxen in the Canadian Arctic Archipelago, and from contemporaneous mortality events and/or population declines among muskoxen in northwestern Alaska and caribou and moose in western Canada. Bacterial genomic diversity differed markedly among these locations; minimal divergence was present among isolates from muskoxen in the Canadian Arctic, while in caribou and moose populations, strains from highly divergent clades were isolated from the same location, or even from within a single carcass. These results indicate that mortalities among northern ungulates are not associated with a single emerging strain of E. rhusiopathiae, and that alternate hypotheses need to be explored. Our study illustrates the value and limitations of bacterial genomic data for discriminating between ecological hypotheses of disease emergence, and highlights the importance of studying emerging pathogens within the broader context of environmental and host factors.
Forde, Taya L.; Orsel, Karin; Zadoks, Ruth N.; Biek, Roman; Adams, Layne G.; Checkley, Sylvia L.; Davison, Tracy; De Buck, Jeroen; Dumond, Mathieu; Elkin, Brett T.; Finnegan, Laura; Macbeth, Bryan J.; Nelson, Cait; Niptanatiak, Amanda; Sather, Shane; Schwantje, Helen M.; van der Meer, Frank; Kutz, Susan J.
Northern ecosystems are currently experiencing unprecedented ecological change, largely driven by a rapidly changing climate. Pathogen range expansion, and emergence and altered patterns of infectious disease, are increasingly reported in wildlife at high latitudes. Understanding the causes and consequences of shifting pathogen diversity and host-pathogen interactions in these ecosystems is important for wildlife conservation, and for indigenous populations that depend on wildlife. Among the key questions are whether disease events are associated with endemic or recently introduced pathogens, and whether emerging strains are spreading throughout the region. In this study, we used a phylogenomic approach to address these questions of pathogen endemicity and spread for Erysipelothrix rhusiopathiae, an opportunistic multi-host bacterial pathogen associated with recent mortalities in arctic and boreal ungulate populations in North America. We isolated E. rhusiopathiae from carcasses associated with large-scale die-offs of muskoxen in the Canadian Arctic Archipelago, and from contemporaneous mortality events and/or population declines among muskoxen in northwestern Alaska and caribou and moose in western Canada. Bacterial genomic diversity differed markedly among these locations; minimal divergence was present among isolates from muskoxen in the Canadian Arctic, while in caribou and moose populations, strains from highly divergent clades were isolated from the same location, or even from within a single carcass. These results indicate that mortalities among northern ungulates are not associated with a single emerging strain of E. rhusiopathiae, and that alternate hypotheses need to be explored. Our study illustrates the value and limitations of bacterial genomic data for discriminating between ecological hypotheses of disease emergence, and highlights the importance of studying emerging pathogens within the broader context of environmental and host factors. PMID
Wyrsch, Ethan R.; Roy Chowdhury, Piklu; Chapman, Toni A.; Charles, Ian G.; Hammond, Jeffrey M.; Djordjevic, Steven P.
Contamination of waste effluent from hospitals and intensive food animal production with antimicrobial residues is an immense global problem. Antimicrobial residues exert selection pressures that influence the acquisition of antimicrobial resistance and virulence genes in diverse microbial populations. Despite these concerns there is only a limited understanding of how antimicrobial residues contribute to the global problem of antimicrobial resistance. Furthermore, rapid detection of emerging bacterial pathogens and strains with resistance to more than one antibiotic class remains a challenge. A comprehensive, sequence-based genomic epidemiological surveillance model that captures essential microbial metadata is needed, both to improve surveillance for antimicrobial resistance and to monitor pathogen evolution. Escherichia coli is an important pathogen causing both intestinal [intestinal pathogenic E. coli (IPEC)] and extraintestinal [extraintestinal pathogenic E. coli (ExPEC)] disease in humans and food animals. ExPEC are the most frequently isolated Gram negative pathogen affecting human health, linked to food production practices and are often resistant to multiple antibiotics. Cattle are a known reservoir of IPEC but they are not recognized as a source of ExPEC that impact human or animal health. In contrast, poultry are a recognized source of multiple antibiotic resistant ExPEC, while swine have received comparatively less attention in this regard. Here, we review what is known about ExPEC in swine and how pig production contributes to the problem of antibiotic resistance. PMID:27379026
Yu, Wei; Wulf, Anja; Yesupriya, Ajay; Clyne, Melinda; Khoury, Muin Joseph; Gwinn, Marta
HuGE Watch is a web-based application for tracking the evolution of published studies on genetic association and human genome epidemiology in near-real time. The application allows users to display temporal trends and spatial distributions as line charts and google maps, providing a quick overview of progress in the field. http://www.hugenavigator.net/HuGENavigator/startPageWatch.do
Huh, K; Ha, Y E; Denning, D W; Peck, K R
Information on the incidence and prevalence of fungal infections is of critical value in public health policy. However, nationwide epidemiological data on fungal infections are scarce, due to a lack of surveillance and funding. The objective of this study was to estimate the disease burden of fungal infections in the Republic of Korea. An actuarial approach using a deterministic model was used for the estimation. Data on the number of populations at risk and the frequencies of fungal infections in those populations were obtained from national statistics reports and epidemiology papers. Approximately 1 million people were estimated to be affected by fungal infections every year. The burdens of candidemia (4.12 per 100,000), cryptococcal meningitis (0.09 per 100,000), and Pneumocystis pneumonia (0.51 per 100,000) in South Korea were estimated to be comparable to those in other countries. The prevalence of chronic pulmonary aspergillosis (22.4 per 100,000) was markedly high, probably due to the high burden of tuberculosis in Korea. The low burdens of allergic bronchopulmonary aspergillosis (56.9 per 100,000) and severe asthma with fungal sensitization (75.1 per 100,000) warrant further study. Oral candidiasis (539 per 100,000) was estimated to affect a much larger population than noted in previous studies. Our work provides valuable insight on the epidemiology of fungal infections; however, additional studies are needed.
Kim, Young-Jo; Chon, Jung-Whan; Lim, Jong-Soo; Song, Bo Ra; Seo, Kun-Ho; Heo, Eun-Jeong; Park, Hyun-Jung; Wee, Seong-Hwan; Oh, Deog Hwan; Moon, Jin-San
We conducted a survey of Salmonella from 8 egg-breaking plants and a farm to determine the prevalence and the source of the bacteria. The contents of 2400 shell eggs (20 eggs per pool), 75 pasteurized liquid egg products, and 120 unpasteurized liquid egg products from 8 egg-breaking plants in South Korea were examined. In liquid egg samples, 4 Salmonella-positive samples from 120 unpasteurized ones (3.3%) and 5 positive samples from 75 pasteurized ones (6.7%) were identified; no eggs were positive for Salmonella among shell egg samples. To trace the source of Salmonella, we revisited the 2 Salmonella-positive plants (plants A and C). We investigated the equipment and environments of the plants and a henhouse (farm A) that supplied shell eggs to plant A, and collected additional liquid eggs and shell eggs from plants A and C. All Salmonella isolates from plant A and the associated farm A, except for a single Typhimurium strain from farm A, were serotyped as Bareilly. Three serovars, including one Bareilly, four Tennessee, and one Richmond, were isolated from plant C. Most Salmonella isolates were susceptible to tested antibiotics. To identify differences between isolates, molecular subtyping by using the automated rep-PCR system was conducted. All Salmonella Bareilly (S. Bareilly) strains from plant A exhibited high similarity, indicating possible contamination by Salmonella strains from the henhouse A. Meanwhile, 2 S. Bareilly strains from plant C, one from liquid egg at the 1st visit and the other from container at the 2nd visit, exhibited identical antibiotic resistance and similar subtyping pattern, but clearly discriminated from the ones of plant A.
Lee, Sang Hyung; Lee, Seung Mi; Lim, Nam Gu; Kim, Hyun Joo; Bae, Sung-Hee; Ock, Minsu; Kim, Un-Na; Lee, Jin Yong; Jo, Min-Woo
Teenage mothers are at high risk for maternal and neonatal complications. This study aimed to evaluate the socioeconomic circumstances of teenage pregnancy, and determine whether these increased risks remained after adjustment for socioeconomic circumstances in Korea. Using the National Health Insurance Corporation database, we selected women who terminated pregnancy, by delivery or abortion, from January 1, 2010 to December 31, 2010. Abortion, delivery type, and maternal complications were defined based on the International Classification of Diseases-10th Revision. We compared teenagers (13-19 years at the time of pregnancy termination) with other age groups and investigated differences based on socioeconomic status, reflected by Medical Aid (MA) and National Health Insurance (NHI) beneficiaries. We used multivariate analysis to define the factors associated with preterm delivery. Among 463,847 pregnancies, 2267 (0.49%) involved teenagers. Teenage mothers were more likely to have an abortion (33.4%) than deliver a baby when compared with other age groups (20.8%; P < 0.001). About 14.4% of teenage mothers had never received prenatal care throughout pregnancy. Among teenage mothers, 61.7% of MA recipients made fewer than 4 prenatal care visits (vs 38.8% of NHI beneficiaries) (P < 0.001). Teenage mothers more often experienced preterm delivery and perineal laceration (P < 0.001). Teenage mothers (<20 years) were 2.47 times more likely to have preterm delivery than older mothers (20-34 years; P < 0.001). Teenage mothers had higher risk of inadequate prenatal care and subsequently of preterm delivery, which remained significantly higher after adjusting for socioeconomic confounding variables and adequacy of prenatal care in Korean teenagers (P < 0.001).
Lee, Yong Hee; Kim, Yu Bin; Koo, Ja Wook
Purpose To investigate the epidemiology, clinical manifestations, investigations and management, and prognosis of patients with Henoch-Schonlein purpura (HSP). Methods We performed a retrospective review of 212 HSP patients under the age of 18 years who were admitted to Inje University Sanggye Paik Hospital between 2004 and 2015. Results The mean age of the HSP patients was 6.93 years, and the ratio of boys to girls was 1.23:1. HSP occurred most frequently in the winter (33.0%) and least frequently in the summer (11.3%). Palpable purpura spots were found in 208 patients (98.1%), and gastrointestinal (GI) and joint symptoms were observed in 159 (75.0%) and 148 (69.8%) patients, respectively. There were 57 patients (26.9%) with renal involvement and 10 patients (4.7%) with nephrotic syndrome. The incidence of renal involvement and nephrotic syndrome was significantly higher in patients with severe GI symptoms and in those over 7 years old. The majority of patients (88.7%) were treated with steroids. There was no significant difference in the incidence of renal involvement or nephrotic syndrome among patients receiving different doses of steroids. Conclusion In this study, the epidemiologic features of HSP in children were similar to those described in previous studies, but GI and joint symptoms manifested more frequently. It is essential to carefully monitor renal involvement and progression to chronic renal disease in patients ≥7 years old and in patients affected by severe GI symptoms. It can be assumed that there is no direct association between early doses of steroids and prognosis. PMID:27738599
Wie, Seong-Heon; So, Byung Hak; Song, Joon Young; Cheong, Hee Jin; Seo, Yu Bin; Choi, Sung Hyuk; Noh, Ji Yun; Baek, Ji Hyeon; Lee, Jin Soo; Kim, Hyo Youl; Kim, Young Keun; Choi, Won Suk; Lee, Jacob; Jeong, Hye Won; Kim, Woo Joo
Background During the 2011/2012 winter influenza season in the Republic of Korea, influenza A (H3N2) was the predominant virus in the first peak period of influenza activity during the second half of January 2012. On the other hand, influenza B was the predominant virus in the second peak period of influenza activity during the second half of March 2012. The objectives of this study were to compare the clinical and epidemiological characteristics of patients with laboratory-confirmed influenza A or influenza B. Methodology/Principal Findings We analyzed data from 2,129 adult patients with influenza-like illnesses who visited the emergency rooms of seven university hospitals in Korea from October 2011 to May 2012. Of 850 patients with laboratory-confirmed influenza, 656 (77.2%) had influenza A (H3N2), and 194 (22.8%) influenza B. Age, and the frequencies of cardiovascular disorders, diabetes, hypertension were significantly higher in patients with influenza A (H3N2) (P<0.05). The frequencies of leukopenia or thrombocytopenia in patients with influenza B at initial presentation were statistically higher than those in patients with influenza A (H3N2) (P<0.05). The rate of hospitalization, and length of hospital stay were statistically higher in patients with influenza A (H3N2) (P<0.05), and of the 79 hospitalized patients, the frequency of diabetes, hypertension, cases having at least one of the comorbid conditions, and the proportion of elderly were significantly higher in patients with influenza A (H3N2) (P<0.05). Conclusions The proportion of males to females and elderly population were significantly higher for influenza A (H3N2) patients group compared with influenza B group. Hypertension, diabetes, chronic lung diseases, cardiovascular disorders, and neuromuscular diseases were independently associated with hospitalization due to influenza. Physicians should assess and treat the underlying comorbid conditions as well as influenza viral infections for the
Li, Xiaoyan; Kong, Mei; Chen, Jinying; Su, Xu; Zou, Ming; Guo, Liru; Li, Lin; Ding, Jianqing
Pandemic influenza A (H1N1) 2009 virus (H1N1pdm09) was a novel tri-assortment virus that emerged in Mexico and North America in 2009 and caused the first influenza pandemic in the 21st century. This study investigated the prevalence pattern and molecular characteristics of H1N1pdm09 in three continuous years from April 2009 to March 2012 in populations of Tianjin, Northeast China. Totally, 3,068 influenza viruses (25.4 %) were detected from 12,089 respiratory specimens. Among them, 41.4 % (1,269/3,068) were H1N1pdm09 positive. 15.1 % (192/1,269) severe respiratory infection cases were H1N1pdm09 positive. H1N1pdm09 was the predominant prevalence subtype in October 2009-March 2010 (69.1 %, 930/1,346) and October 2010-March 2011 (42.1 %, 220/523). Eight isolated H1N1pdm09 viruses from severe infection/death cases in three different years were selected to sequence the whole genome through splicing the sequences following 46 PCRs. HA sequences of seven H1N1pdm09 isolates from mild infection cases were detected. Phylogenetic analysis showed that HA, NA, M, NP and NS genes of H1N1pdm09 viruses gathered together with swine influenza A (H1N1), whereas PB2 and PA genes originated from avian influenza virus, and PB1 gene originated from human seasonal influenza virus. Identity analysis indicated that all the genes were highly conserved. Compared with vaccine strain A/California/07/2009(H1N1), the maximal mutation gene was HA (0.7-2.6 %), then NA (0.6-1.7 %), last one was M (mutation rate 0-0.6 %). More site substitutions were observed in 2011 isolates than in 2009 and 2010 isolates of HA (p = 0.002), NA (p = 0.003) and PA (p = 0.001) proteins. The amino acid substitution rates were varied among eight gene segments, ranging from 7.39 × 10(-4) for PB2 to 7.40 × 10(-3) for NA. The higher d N / d S rates were observed in HA, PA and NS segments in H1N1pdm09 in Tianjin. Three HA amino acid site substitutions occurred at the HA receptor-binding sites and
Carty, Cara L.; Franceschini, Nora; Fernández-Rhodes, Lindsay; Young, Alicia; Cheng, Iona; Ritchie, Marylyn D.; Haiman, Christopher A.; Wilkens, Lynne; ChunyuanWu; Matise, Tara C.; Carlson, Christopher S.; Brennan, Kathleen; Park, Amy; Rajkovic, Aleksandar; Hindorff, Lucia A.
Age at menarche (AM) and age at natural menopause (ANM) define the boundaries of the reproductive lifespan in women. Their timing is associated with various diseases, including cancer and cardiovascular disease. Genome-wide association studies have identified several genetic variants associated with either AM or ANM in populations of largely European or Asian descent women. The extent to which these associations generalize to diverse populations remains unknown. Therefore, we sought to replicate previously reported AM and ANM findings and to identify novel AM and ANM variants using the Metabochip (n = 161,098 SNPs) in 4,159 and 1,860 African American women, respectively, in the Women’s Health Initiative (WHI) and Atherosclerosis Risk in Communities (ARIC) studies, as part of the Population Architecture using Genomics and Epidemiology (PAGE) Study. We replicated or generalized one previously identified variant for AM, rs1361108/CENPW, and two variants for ANM, rs897798/BRSK1 and rs769450/APOE, to our African American cohort. Overall, generalization of the majority of previously-identified variants for AM and ANM, including LIN28B and MCM8, was not observed in this African American sample. We identified three novel loci associated with ANM that reached significance after multiple testing correction (LDLR rs189596789, p = 5×10−08; KCNQ1 rs79972789, p = 1.9×10−07; COL4A3BP rs181686584, p = 2.9×10−07). Our most significant AM association was upstream of RSF1, a gene implicated in ovarian and breast cancers (rs11604207, p = 1.6×10−06). While most associations were identified in either AM or ANM, we did identify genes suggestively associated with both: PHACTR1 and ARHGAP42. The lack of generalization coupled with the potentially novel associations identified here emphasize the need for additional genetic discovery efforts for AM and ANM in diverse populations. PMID:23424626
Dumitrescu, Logan; Carty, Cara L.; Taylor, Kira; Schumacher, Fredrick R.; Hindorff, Lucia A.; Ambite, José L.; Anderson, Garnet; Best, Lyle G.; Brown-Gentry, Kristin; Bůžková, Petra; Carlson, Christopher S.; Cochran, Barbara; Cole, Shelley A.; Devereux, Richard B.; Duggan, Dave; Eaton, Charles B.; Fornage, Myriam; Franceschini, Nora; Haessler, Jeff; Howard, Barbara V.; Johnson, Karen C.; Laston, Sandra; Kolonel, Laurence N.; Lee, Elisa T.; MacCluer, Jean W.; Manolio, Teri A.; Pendergrass, Sarah A.; Quibrera, Miguel; Shohet, Ralph V.; Wilkens, Lynne R.; Haiman, Christopher A.; Le Marchand, Loïc; Buyske, Steven; Kooperberg, Charles; North, Kari E.; Crawford, Dana C.
For the past five years, genome-wide association studies (GWAS) have identified hundreds of common variants associated with human diseases and traits, including high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), and triglyceride (TG) levels. Approximately 95 loci associated with lipid levels have been identified primarily among populations of European ancestry. The Population Architecture using Genomics and Epidemiology (PAGE) study was established in 2008 to characterize GWAS–identified variants in diverse population-based studies. We genotyped 49 GWAS–identified SNPs associated with one or more lipid traits in at least two PAGE studies and across six racial/ethnic groups. We performed a meta-analysis testing for SNP associations with fasting HDL-C, LDL-C, and ln(TG) levels in self-identified European American (∼20,000), African American (∼9,000), American Indian (∼6,000), Mexican American/Hispanic (∼2,500), Japanese/East Asian (∼690), and Pacific Islander/Native Hawaiian (∼175) adults, regardless of lipid-lowering medication use. We replicated 55 of 60 (92%) SNP associations tested in European Americans at p<0.05. Despite sufficient power, we were unable to replicate ABCA1 rs4149268 and rs1883025, CETP rs1864163, and TTC39B rs471364 previously associated with HDL-C and MAFB rs6102059 previously associated with LDL-C. Based on significance (p<0.05) and consistent direction of effect, a majority of replicated genotype-phentoype associations for HDL-C, LDL-C, and ln(TG) in European Americans generalized to African Americans (48%, 61%, and 57%), American Indians (45%, 64%, and 77%), and Mexican Americans/Hispanics (57%, 56%, and 86%). Overall, 16 associations generalized across all three populations. For the associations that did not generalize, differences in effect sizes, allele frequencies, and linkage disequilibrium offer clues to the next generation of association studies for these traits. PMID:21738485
Cho, Nam H; Oh, Tae Jung; Kim, Kyoung Min; Choi, Sung Hee; Lee, Jae Ho; Park, Kyong Soo; Jang, Hak Chul; Kim, Jong Yeol; Lee, Hong Kyu; Lim, Soo
Neck circumference, a proxy for upper-body fat, may be a unique fat depot that indicates metabolic risk beyond whole body fat. We investigated whether neck circumference is associated with development of diabetes mellitus (DM) in a subset of data with Korean Genome and Epidemiology Study (n = 3521, age range = 42-71 years). Nondiabetic subjects at the baseline were categorized into 4 groups (Q1-Q4) according to their neck circumference. Parameters related with β-cell function and insulin resistance including Epworth sleepiness scale and snoring habit were examined. The development of DM was confirmed biannually based on a 75-g oral glucose tolerance test. Over the 10 years, 2623 (74.5%) among 3521 subjects were followed-up. Among them, 632 (24.1%) developed DM. The incidence of DM increased from 17.6% in Q1 to 18.2% in Q2, to 25.4% in Q3, and to 36.0% in Q4 (P < 0.001). After adjusting for most risk factors related with DM, the relative risks of DM development were 0.989 (95% confidence interval, 0.638-1.578), 1.660 (1.025-2.687), and 1.746 (1.037-2.942) in men and 0.939 (0.540-1.769), 1.518 (0.808-2.853), and 2.077 (1.068-4.038) in women in Q2, Q3, and Q4, respectively when compared to Q1. This finding indicates negative impact from large neck circumference in the development of DM.
Choi, Hansol; Kim, Hyeon Chang; Lee, Joo Young; Lee, Ju-Mi; Choi, Dong Phil; Suh, Il
Background/Aims Sleep duration affects health in various ways. The objective of this study was to investigate the associations of sleep duration with chronic kidney disease (CKD) in a Korean adult population. Methods This cross-sectional analysis was conducted for total of 1,360 participants who completed baseline health examinations for the Korean Genome and Epidemiology Study-Kangwha study in 2010 to 2011. Sleep habits were measured by an interviewer-assisted questionnaire. Sleep duration was calculated based on the number of hours per day participants had slept over the past 1 year. CKD was defined as either proteinuria or estimated glomerular filtration rate (eGFR) < 60 mL/min/1.73 m2. Multiple logistic regression models were applied to examine associations between sleep duration and CKD. Results Women with very long sleep duration (≥ 9 hours/day) were at significantly increased odds for having high serum creatinine (odds ratio [OR], 2.936; 95% confidence interval [CI], 1.176 to 7.326), low eGFR (OR, 3.320; 95% CI, 1.372 to 8.034), and CKD (OR, 3.112; 95% CI, 1.315 to 7.363), compared those with a typical sleep duration (7 to < 8 hours/day), after adjusting for sociodemographic status, socioeconomic status, health behaviors, comorbidities, and sleep quality. Among women, for every 1 hour increase in sleep duration per day, there was a 24.6% increase in the presence of CKD (OR, 1.246; 95% CI, 1.019 to 1.523). However, among men, sleep duration was not significantly associated with CKD. Conclusions Very long sleep duration was independently associated with a higher prevalence of CKD among Korean women. Gender may influence this association. PMID:28192891
Choe, Young June; Lee, Hyunju; Lee, Hoan Jong; Choi, Eun Hwa
Antiviral therapy has an important role in the treatment and chemoprophylaxis of influenza. At present, two classes of antiviral agents, adamantanes and neuraminidase inhibitors, are available for the treatment and chemoprophylaxis of influenza in Korea. Because of the widespread resistance against adamantanes, neuraminidase inhibitors are mainly used. Because each country has a unique epidemiology of influenza, the proper use of antiviral agents should be determined based on local data. Decisions on the clinical practice in the treatment of influenza in South Korea are guided by the local surveillance data, practice guidelines, health insurance system and the resistance patterns of the circulating influenza viruses. This review highlights the role of antiviral agents in the treatment and outcome of influenza in Korea by providing comprehensive information of their clinical usage in Korea.
Ichiyama, S; Ohta, M; Shimokata, K; Kato, N; Takeuchi, J
In this study, we have compared genomic DNA fingerprintings among isolates of methicillin-resistant Staphylococcus aureus (MRSA) by using pulsed-field gel electrophoresis (PFGE). Chromosomal fragments digested with SmaI were most suitable for the PFGE separation. SmaI cut genomic DNA into 15 to 20 fragments whose sizes ranged from about 30 to 1,500 kb. Thirty-one distinctive fragment patterns were identified in 111 infecting and colonizing MRSA isolates from six different hospitals in Japan. On the basis of the genomic typing by PFGE, we performed an epidemiological investigation of an outbreak of nosocomial MRSA infections among inpatients in Nagoya University Hospital. Ten types of chromosomal digestion were identified in the 20 strains isolated from 18 infected patients and 1 from colonized hospital personnel. According to the restriction patterns, we found that four types of these strains had caused epidemic infections among 13 patients in the outbreak. Two types (types 1 and 4) of the strains were involved in the death of five patients. The other infections were sporadic. The clarity and polymorphism of the chromosomal digestion patterns enabled us to discriminate between isolates which could not be differentiated by antibiogram or plasmid analysis. Classification of the genomic DNA fingerprinting patterns by PFGE is therefore proposed as a useful method for investigating the source, transmission, and spread of nosocomial MRSA infections. Images PMID:1757534
High-quality draft genome sequence of Flavobacterium suncheonense GH29-5(T) (DSM 17707(T)) isolated from greenhouse soil in South Korea, and emended description of Flavobacterium suncheonense GH29-5(T).
Tashkandy, Nisreen; Sabban, Sari; Fakieh, Mohammad; Meier-Kolthoff, Jan P; Huang, Sixing; Tindall, Brian J; Rohde, Manfred; Baeshen, Mohammed N; Baeshen, Nabih A; Lapidus, Alla; Copeland, Alex; Pillay, Manoj; Reddy, T B K; Huntemann, Marcel; Pati, Amrita; Ivanova, Natalia; Markowitz, Victor; Woyke, Tanja; Göker, Markus; Klenk, Hans-Peter; Kyrpides, Nikos C; Hahnke, Richard L
Flavobacterium suncheonense is a member of the family Flavobacteriaceae in the phylum Bacteroidetes. Strain GH29-5(T) (DSM 17707(T)) was isolated from greenhouse soil in Suncheon, South Korea. F. suncheonense GH29-5(T) is part of the G enomic E ncyclopedia of B acteria and A rchaea project. The 2,880,663 bp long draft genome consists of 54 scaffolds with 2739 protein-coding genes and 82 RNA genes. The genome of strain GH29-5(T) has 117 genes encoding peptidases but a small number of genes encoding carbohydrate active enzymes (51 CAZymes). Metallo and serine peptidases were found most frequently. Among CAZymes, eight glycoside hydrolase families, nine glycosyl transferase families, two carbohydrate binding module families and four carbohydrate esterase families were identified. Suprisingly, polysaccharides utilization loci (PULs) were not found in strain GH29-5(T). Based on the coherent physiological and genomic characteristics we suggest that F. suncheonense GH29-5(T) feeds rather on proteins than saccharides and lipids.
Over the past several decades, the prevalence of obesity has increased dramatically worldwide and is increasing not only in developed countries, but also in developing countries. This increase may lead to an increase in the incidence of chronic diseases throughout the lifespan. In Korean children and adolescents, the prevalence of obesity increased from 6.8% in 1998 to 10.0% in 2013. Obesity is a state that more commonly influences children and adolescents of lower socioeconomic status (SES) than those with a higher SES. However, the prevalence of metabolic syndrome in a nationally representative sample of Korean adolescents decreased from 1998 to 2012. According to the Diabetes Fact Sheet of the Korean Diabetes Association, the prevalence of type 2 diabetes among children aged 18 years or younger was 153.5 per 100,000 in 2006 and 205.0 per 100,000 in 2013. Obesity is a complex disease influenced by many interacting factors, such as adipocytokines, lipopolysaccharide-binding protein, adenovirus 36 infection, birth weight, lifestyle, and endocrine-disrupting chemicals. Obesity in youth can adversely impact practically every organ system and lead to serious consequences, such as metabolic, gastrointestinal, pulmonary, cardiovascular, and psychosocial complications. Therefore, coordinated efforts by governments, organizations, communities, and individuals are needed to prevent and treat childhood obesity. In particular, a long-term policy to improve the social environment will also be necessary. PMID:27834078
Morré, S A; Ouburg, S; Peña, A S; Brand, A
Chlamydia trachomatis infections are responsible for the world's leading cause of blindness (trachoma) and its most prevalent sexually transmitted disease, which is strongly associated with pelvic inflammatory disease, ectopic pregnancy and tubal infertility. Twin study-based findings of members of EpiGenChlamydia Consortium estimate that there is a 40% genetic predisposition to C. trachomatis infections. It is likely that the advances in human genomics will help to unravel the genetic predisposition at the gene level and will help to define a genetic fingerprint that can be used as a marker for this predisposition. The information gathered to date suggests that this predisposition and the factors contributing to prognosis are multifactorial. The EpiGenChlamydia Consortium aims to structure transnational research to such a degree that comparative genomics and genetic epidemiology can be performed in large numbers of unrelated individuals. Biobanking and data-warehouse building are the most central deliverables of the Coordination Action of the Consortium in Functional Genomics Research. In addition, the collective synergy acquired in this Coordination Action will allow for the generation of scientific knowledge on the C. trachomatis-host interaction, knowledge on the genetic predisposition to C. trachomatis infection and the development of tools for early detection of a predisposition to C. trachomatis infection and its complications. This review summarizes the consortium aims and progress, and future perspectives and directions.
The Cancer Epidemiology Matters blog helps foster a dialogue between the National Cancer Institute's (NCI) Epidemiology and Genomics Research Program (EGRP), extramural researchers, and other individuals, such as clinicians, community partners, and advocates, who are interested in cancer epidemiology and genomics.
The Cancer Epidemiology Matters blog helps foster a dialogue between the National Cancer Institute's (NCI) Epidemiology and Genomics Research Program (EGRP), extramural researchers, and other individuals, such as clinicians, community partners, and advocates, who are interested in cancer epidemiology and genomics.
Glaser, Linda; Carstensen, Michelle; Shaw, Sheryl; Robbe-Austerman, Suelee; Wunschmann, Arno; Grear, Dan; Stuber, Tod; Thomsen, Bruce
Bovine tuberculosis (bTB) was discovered in a Minnesota cow through routine slaughter surveillance in 2005 and the resulting epidemiological investigation led to the discovery of infection in both cattle and white-tailed deer in the state. From 2005 through 2009, a total of 12 beef cattle herds and 27 free-ranging white-tailed deer (Odocoileus virginianus) were found infected in a small geographic region of northwestern Minnesota. Genotyping of isolates determined both cattle and deer shared the same strain of bTB, and it was similar to types found in cattle in the southwestern United States and Mexico. Whole genomic sequencing confirmed the introduction of this infection into Minnesota was recent, with little genetic divergence. Aggressive surveillance and management efforts in both cattle and deer continued from 2010–2012; no additional infections were discovered. Over 10,000 deer were tested and 705 whole herd cattle tests performed in the investigation of this outbreak. PMID:26785113
Glaser, Linda; Carstensen, Michelle; Shaw, Sheryl; Robbe-Austerman, Suelee; Wunschmann, Arno; Grear, Dan; Stuber, Tod; Thomsen, Bruce
Bovine tuberculosis (bTB) was discovered in a Minnesota cow through routine slaughter surveillance in 2005 and the resulting epidemiological investigation led to the discovery of infection in both cattle and white-tailed deer in the state. From 2005 through 2009, a total of 12 beef cattle herds and 27 free-ranging white-tailed deer (Odocoileus virginianus) were found infected in a small geographic region of northwestern Minnesota. Genotyping of isolates determined both cattle and deer shared the same strain of bTB, and it was similar to types found in cattle in the southwestern United States and Mexico. Whole genomic sequencing confirmed the introduction of this infection into Minnesota was recent, with little genetic divergence. Aggressive surveillance and management efforts in both cattle and deer continued from 2010-2012; no additional infections were discovered. Over 10,000 deer were tested and 705 whole herd cattle tests performed in the investigation of this outbreak.
Smeltzer, M S; Gillaspy, A F; Pratt, F L; Thames, M D
We used a genomic fingerprinting protocol to characterize 59 Staphylococcus aureus strains and a single S. intermedius isolate, all of which were previously typed by 13 different methods (F. C. Tenover et al., J. Clin. Microbiol. 32:407-415, 1994). These 60 strains were divided into three groups of 20 strains each, with each group including internal controls. Two of the three groups (groups SB and SC) included 29 strains from four relatively well-defined outbreaks. The epidemiological relationships of the strains in the third group (group SA) were unclear. Fingerprints were established by Southern blotting with HaeIII-digested genomic DNA and a probe mixture consisting of DNA fragments corresponding to the S. aureus collagen adhesin (cna), fibronectin-binding protein (fnbA and fnbB), and beta-toxin (hlb) genes. An unambiguous fingerprint was obtained for all S. aureus isolates. No hybridization signal was observed with S. intermedius. Twenty-seven of the 29 related strains in the SB and SC groups were correctly identified as belonging to one of the four epidemiologically related groups. Our protocol was less successful with respect to the exclusion of unrelated strains. Specifically, only 6 of 11 unrelated strains in the SB and SC groups had a fingerprint that was distinct by comparison to the fingerprints of the outbreak strains. Nevertheless, our protocol was relatively accurate by comparison to the accuracies of the other methods and was one of only six methods that accurately identified all of the repetitive strains included as internal controls.
Rodrigo-Torres, Lidia; Pujalte, María J.; Arahal, David R.
We report the draft genome sequence and annotation of Leisingera aquaemixtae CECT 8399T (DDBJ/EMBL/GenBank accession number CYSR00000000) which comprises 4,614,060 bp, 4313 protein coding genes, 54 tRNA coding genes and 7 rRNA coding genes. General findings of the annotated genome, such as pigment indigoidine operon, phenylacetate oxidation genes or predictable number of replicons, are commented in comparison to other Leisingera species. Average Nucleotide Identity between available genomes of type strains of species of Leisingera and Phaeobacter genera has been calculated to evaluate its current classification. PMID:26981415
Crotta, M.; Wall, B.; Good, L.; O'Brien, S. J.; Guitian, J.
Foodborne infection is a result of exposure to complex, dynamic food systems. The efficiency of foodborne infection is driven by ongoing shifts in genetic machinery. Next-generation sequencing technologies can provide high-fidelity data about the genetics of a pathogen. However, food safety surveillance systems do not currently provide similar high-fidelity epidemiological metadata to associate with genetic data. As a consequence, it is rarely possible to transform genetic data into actionable knowledge that can be used to genuinely inform risk assessment or prevent outbreaks. Big data approaches are touted as a revolution in decision support, and pose a potentially attractive method for closing the gap between the fidelity of genetic and epidemiological metadata for food safety surveillance. We therefore developed a simple food chain model to investigate the potential benefits of combining ‘big’ data sources, including both genetic and high-fidelity epidemiological metadata. Our results suggest that, as for any surveillance system, the collected data must be relevant and characterize the important dynamics of a system if we are to properly understand risk: this suggests the need to carefully consider data curation, rather than the more ambitious claims of big data proponents that unstructured and unrelated data sources can be combined to generate consistent insight. Of interest is that the biggest influencers of foodborne infection risk were contamination load and processing temperature, not genotype. This suggests that understanding food chain dynamics would probably more effectively generate insight into foodborne risk than prescribing the hazard in ever more detail in terms of genotype.
... Services released a report identifying gaps in the regulation, oversight, and usefulness of genetic testing. They expressed ... December 20, 2016 Content source: Center for Surveillance, Epidemiology and Laboratory Services (CSELS) , Public Health Genomics Email ...
Tajima, Shigeru; Nakayama, Eri; Kotaki, Akira; Moi, Meng Ling; Ikeda, Makiko; Yagasaki, Kazumi; Saito, Yuka; Shibasaki, Ken-Ichi; Saijo, Masayuki; Takasaki, Tomohiko
Cases of autochthonous infections of dengue virus type 1 (DENV-1) were detected in Japan after a 70-year period devoid of dengue outbreaks. We previously showed that E gene sequences are identical in 11 of the 12 DENV-1 strains autochthonous to Japan. However, the E sequence represents only 14% of the DENV-1 genome. In the present study, we have sequenced the entire genome of 6 autochthonous DENV-1 strains that were isolated from patients during the 2014 outbreak. Sequencing of 5 Yoyogi group strains with identical E sequences and 1 Shizuoka strain with a different E sequence revealed that the first Yoyogi group strain differed from the Shizuoka strain by 18 amino acid residues. Furthermore, 2 Yoyogi group strains had different genomic sequences while the other 3 had identical genomes. Phylogenetic analyses indicated that the Hyogo strain, a Yoyogi group strain, was the first to diverge from the other 4 Yoyogi group strains. The E gene sequence of the Yoyogi group strains exhibits the highest homology to those of the strains isolated in Malaysia and Singapore between 2013 and 2014. The patient infected with the Hyogo strain visited Malaysia before the onset of dengue fever, suggesting that this was a case of dengue infection imported from Malaysia.
Burall, Laurel S.; Grim, Christopher J.; Mammel, Mark K.; Datta, Atin R.
In an effort to build a comprehensive genomic approach to food safety challenges, the FDA has implemented a whole genome sequencing effort, GenomeTrakr, which involves the sequencing and analysis of genomes of foodborne pathogens. As a part of this effort, we routinely sequence whole genomes of Listeria monocytogenes (Lm) isolates associated with human listeriosis outbreaks, as well as those isolated through other sources. To rapidly establish genetic relatedness of these genomes, we evaluated tetranucleotide frequency analysis via the JSpecies program to provide a cursory analysis of strain relatedness. The JSpecies tetranucleotide (tetra) analysis plots standardized (z-score) tetramer word frequencies of two strains against each other and uses linear regression analysis to determine similarity (r2). This tool was able to validate the close relationships between outbreak related strains from four different outbreaks. Included in this study was the analysis of Lm strains isolated during the recent caramel apple outbreak and stone fruit incident in 2014. We identified that many of the isolates from these two outbreaks shared a common 4b variant (4bV) serotype, also designated as IVb-v1, using a qPCR protocol developed in our laboratory. The 4bV serotype is characterized by the presence of a 6.3 Kb DNA segment normally found in serotype 1/2a, 3a, 1/2c and 3c strains but not in serotype 4b or 1/2b strains. We decided to compare these strains at a genomic level using the JSpecies Tetra tool. Specifically, we compared several 4bV and 4b isolates and identified a high level of similarity between the stone fruit and apple 4bV strains, but not the 4b strains co-identified in the caramel apple outbreak or other 4b or 4bV strains in our collection. This finding was further substantiated by a SNP-based analysis. Additionally, we were able to identify close relatedness between isolates from clinical cases from 1993–1994 and a single case from 2011 as well as links between
Du, Pengcheng; Zheng, Han; Zhou, Jieping; Lan, Ruiting; Ye, Changyun; Jing, Huaiqi; Jin, Dong; Cui, Zhigang; Bai, Xuemei; Liang, Jianming; Liu, Jiantao; Xu, Lei; Zhang, Wen; Chen, Chen
Streptococcus suis sequence type 7 emerged and caused 2 of the largest human infection outbreaks in China in 1998 and 2005. To determine the major risk factors and source of the infections, we analyzed whole genomes of 95 outbreak-associated isolates, identified 160 single nucleotide polymorphisms, and classified them into 6 clades. Molecular clock analysis revealed that clade 1 (responsible for the 1998 outbreak) emerged in October 1997. Clades 2–6 (responsible for the 2005 outbreak) emerged separately during February 2002–August 2004. A total of 41 lineages of S. suis emerged by the end of 2004 and rapidly expanded to 68 genome types through single base mutations when the outbreak occurred in June 2005. We identified 32 identical isolates and classified them into 8 groups, which were distributed in a large geographic area with no transmission link. These findings suggest that persons were infected in parallel in respective geographic sites. PMID:27997331
Epidemiology of Type 1 Diabetes Mellitus in Korea through an Investigation of the National Registration Project of Type 1 Diabetes for the Reimbursement of Glucometer Strips with Additional Analyses Using Claims Data
Song, Sun Ok; Nam, Joo Young; Park, Kyeong Hye; Yoon, Ji-Hae; Son, Kyung-Mi; Ko, Young; Lim, Dong-Ha
Background The aim of this study was to estimate the prevalence and incidence of type 1 diabetes mellitus (T1DM) in Korea. In addition, we planned to do a performance analysis of the Registration Project of Type 1 diabetes for the reimbursement of consumable materials. Methods To obtain nationwide data on the incidence and prevalence of T1DM, we extracted claims data from July 2011 to August 2013 from the Registration Project of Type 1 diabetes on the reimbursement of consumable materials in the National Health Insurance (NHI) Database. For a more detailed analysis of the T1DM population in Korea, stratification by gender, age, and area was performed, and prevalence and incidence were calculated. Results Of the 8,256 subjects enrolled over the 26 months, the male to female ratio was 1 to 1.12, the median age was 37.1 years, and an average of 136 new T1DM patients were registered to the T1DM registry each month, resulting in 1,632 newly diagnosed T1DM patients each year. We found that the incidence rate of new T1DM cases was 3.28 per 100,000 people. The average proportion of T1DM patients compared with each region's population was 0.0125%. The total number of insurance subscribers under the universal compulsory NHI in Korea was 49,662,097, and the total number of diabetes patients, excluding duplication, was 3,762,332. Conclusion The prevalence of T1DM over the course of the study was approximately 0.017% to 0.021% of the entire population of Korea, and the annual incidence of T1DM was 3.28:100,000 overall and 3.25:100,000 for Koreans under 20 years old. PMID:26912154
Kwon, Taesoo; Yang, Ji Woo; Lee, Sanghyun; Yun, Mi-ran; Yoo, Won Gi; Kim, Hwa Su
The prevalence of Klebsiella pneumoniae coproducing carbapenemase metallo-β-lactamase 1 (NDM-1) and OXA-48 has been increasing globally since 2013. The complete genome of KP617 was sequenced and assembled into a circular chromosome and two plasmids. This sequence provides the genetic background for understanding the evolution of carbapenemase genes in K. pneumoniae KP617. PMID:26769936
Gu, Se Hun; Song, Dong Hyun; Lee, Daesang; Huh, Kyungmin; Yoo, Hongseok; Oh, Hong Sang; Jung, Jaehun; Woo, Koung In; Kim, Mirang; Seog, Woong; Hwang, Il-Ung
ABSTRACT Human adenovirus (HAdV) (genus Mastadenovirus; family Adenoviridae) serotype 55 is a reemerging pathogen associated with acute respiratory disease. Here, we report the complete genome sequence of HAdV-55 strain AFMC 16-0011, isolated from a military recruit, using next-generation sequencing technology. PMID:28280019
opportunity to rebuild South Korea . He saw it as “something almost unique in history. It is the opportunity of an army in a foreign land to contribute...problems. The North Korean invasion in 1950 wedded South Korea to the United States and confronted the United States with the enormous task of...elections in Korea .8 After failing to achieve agreement to peninsula-wide elections, the United Nations sponsored elections in South
Scott, Terence P.; Fischer, Melina; Khaiseb, Siegfried; Freuling, Conrad; Höper, Dirk; Hoffmann, Bernd; Markotter, Wanda; Müller, Thomas; Nel, Louis H.
Rabies in kudu is unique to Namibia and two major peaks in the epizootic have occurred since it was first noted in 1977. Due to the large numbers of kudu that were affected, it was suspected that horizontal transmission of rabies occurs among kudu and that rabies was being maintained independently within the Namibian kudu population – separate from canid cycles, despite geographic overlap. In this study, it was our aim to show, through phylogenetic analyses, that rabies was being maintained independently within the Namibian kudu population. We also tested, through complete genome sequencing of four rabies virus isolates from jackal and kudu, whether specific mutations occurred in the virus genome due to host adaptation. We found the separate grouping of all rabies isolates from kudu to those of any other canid species in Namibia, suggesting that rabies was being maintained independently in kudu. Additionally, we noted several mutations unique to isolates from kudu, suggesting that these mutations may be due to the adaptation of rabies to a new host. In conclusion, we show clear evidence that rabies is being maintained independently in the Namibian kudu population – a unique phenomenon with ecological and economic impacts. PMID:23527015
Holmes, A; McAllister, G; McAdam, P R; Hsien Choi, S; Girvan, K; Robb, A; Edwards, G; Templeton, K; Fitzgerald, J R
The EMRSA-15 clone is a major cause of nosocomial methicillin-resistant Staphylococcus aureus (MRSA) infections in the UK and elsewhere but existing typing methodologies have limited capacity to discriminate closely related strains, and are often poorly reproducible between laboratories. Here, we report the design, development and validation of a genome-wide single nucleotide polymorphism (SNP) typing method and compare it to established methods for typing of EMRSA-15. In order to identify discriminatory SNPs, the genomes of 17 EMRSA-15 strains, selected to represent the breadth of genotypic and phenotypic diversity of EMRSA-15 isolates in Scotland, were determined and phylogenetic reconstruction was carried out. In addition to 17 phylogenetically informative SNPs, five binary markers were included to form the basis of an EMRSA-15 genotyping assay. The SNP-based typing assay was as discriminatory as pulsed-field gel electrophoresis, and significantly more discriminatory than staphylococcal protein A (spa) typing for typing of a representative panel of diverse EMRSA-15 strains, isolates from two EMRSA-15 hospital outbreak investigations, and a panel of bacteraemia isolates obtained in healthcare facilities in the east of Scotland during a 12-month period. The assay is a rapid, and reproducible approach for epidemiological analysis of EMRSA-15 clinical isolates in Scotland. Unlike established methods the DNA sequence-based method is ideally suited for inter-laboratory comparison of identified genotypes, and its flexibility lends itself to supplementation with additional SNPs or markers for the identification of novel S. aureus strains in other regions of the world.
Phylogenetic Analyses of Shigella and Enteroinvasive Escherichia coli for the Identification of Molecular Epidemiological Markers: Whole-Genome Comparative Analysis Does Not Support Distinct Genera Designation.
Pettengill, Emily A; Pettengill, James B; Binet, Rachel
As a leading cause of bacterial dysentery, Shigella represents a significant threat to public health and food safety. Related, but often overlooked, enteroinvasive Escherichia coli (EIEC) can also cause dysentery. Current typing methods have limited ability to identify and differentiate between these pathogens despite the need for rapid and accurate identification of pathogens for clinical treatment and outbreak response. We present a comprehensive phylogeny of Shigella and EIEC using whole genome sequencing of 169 samples, constituting unparalleled strain diversity, and observe a lack of monophyly between Shigella and EIEC and among Shigella taxonomic groups. The evolutionary relationships in the phylogeny are supported by analyses of population structure and hierarchical clustering patterns of translated gene homolog abundance. Lastly, we identified a panel of 404 single nucleotide polymorphism (SNP) markers specific to each phylogenetic cluster for more accurate identification of Shigella and EIEC. Our findings show that Shigella and EIEC are not distinct evolutionary groups within the E. coli genus and, thus, EIEC as a group is not the ancestor to Shigella. The multiple analyses presented provide evidence for reconsidering the taxonomic placement of Shigella. The SNP markers offer more discriminatory power to molecular epidemiological typing methods involving these bacterial pathogens.
The National Cancer Institute frequently receives questions from investigators for examples of successfully funded grant applications. Several investigators agreed to let the Epidemiology and Genomics Research Program post excerpts of their grant applications online.
Background High-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), and triglyceride (TG) levels are influenced by both genes and the environment. Genome-wide association studies (GWAS) have identified ~100 common genetic variants associated with HDL-C, LDL-C, and/or TG levels, mostly in populations of European descent, but little is known about the modifiers of these associations. Here, we investigated whether GWAS-identified SNPs for lipid traits exhibited heterogeneity by sex in the Population Architecture using Genomics and Epidemiology (PAGE) study. Results A sex-stratified meta-analysis was performed for 49 GWAS-identified SNPs for fasting HDL-C, LDL-C, and ln(TG) levels among adults self-identified as European American (25,013). Heterogeneity by sex was established when phet < 0.001. There was evidence for heterogeneity by sex for two SNPs for ln(TG) in the APOA1/C3/A4/A5/BUD13 gene cluster: rs28927680 (phet = 7.4x10-7) and rs3135506 (phet = 4.3x10-4), one SNP in PLTP for HDL levels (rs7679; phet = 9.9x10-4), and one in HMGCR for LDL levels (rs12654264; phet = 3.1x10-5). We replicated heterogeneity by sex in five of seventeen loci previously reported by genome-wide studies (binomial p = 0.0009). We also present results for other racial/ethnic groups in the supplementary materials, to provide a resource for future meta-analyses. Conclusions We provide further evidence for sex-specific effects of SNPs in the APOA1/C3/A4/A5/BUD13 gene cluster, PLTP, and HMGCR on fasting triglyceride levels in European Americans from the PAGE study. Our findings emphasize the need for considering context-specific effects when interpreting genetic associations emerging from GWAS, and also highlight the difficulties in replicating interaction effects across studies and across racial/ethnic groups. PMID:23634756
In an effort to broaden access and facilitate efficient data sharing, the Epidemiology and Genomics Research Program (EGRP) has created the Cancer Epidemiology Data Repository (CEDR), a centralized, controlled-access database, where Investigators can deposit individual-level de-identified observational cancer datasets.
Perrotta, D; Rodero, L; Demkura, H; Canteros, C; Davel, G
During the past decades, several studies have reported an increase in the incidence of nosocomial candidosis. In a prospective study, performed at the Departamento de Micología, INEI, ANLIS Dr. C. G. Malbrán and the Servicio de Neonatología and Microbiología, Hospital de Niños Sor María Ludovica, from October 1995 to December 1996, 167 patients with candidosis were detected. Candida species isolated were C. albicans (53.1%), C. parapsilosis (26.5%) and C. tropicalis (14.8%). The aim of this work was to characterize the clinical C. parapsilosis isolates from pediatric patients hospitalized in two neonatal intensive care units from the same hospital and to evaluate the usefulness of electrophoretic karyotype (EK) and restriction endonuclease analysis of genomic DNA (REAG) using a low frequency digestion enzyme. EK of all isolates disclosed 12 banding patterns and REAG with endonuclease Sfi I showed only 5 groups. However, isolates from the control group could not be separated from the clinical isolates. The isolates within each dendogram group for EK or REAG were apparently unrelated. Our results show that EK yields better results than REAG, but that it falls short of the desired discrimination, which suggests that these techniques do not seem to be useful for studying nosocomial C. parapsilosis outbreaks.
High-throughput molecular screening is required to investigate the origin and diffusion of antimicrobial resistance in pathogen outbreaks. The most frequent cause of human infection is Escherichia coli, which is dominated by sequence type 131 (ST131)—a set of rapidly radiating pandemic clones. The highly infectious clades of ST131 originated firstly by a mutation enhancing conjugation and adhesion. Secondly, single-nucleotide polymorphisms occurred enabling fluoroquinolone-resistance, which is near-fixed in all ST131. Thirdly, broader resistance through beta-lactamases has been gained and lost frequently, symptomatic of conflicting environmental selective effects. This flexible approach to gene exchange is worrying and supports the proposition that ST131 will develop an even wider range of plasmid and chromosomal elements promoting antimicrobial resistance. To stop ST131, deep genome sequencing is required to understand the origin, evolution and spread of antimicrobial resistance genes. Phylogenetic methods that decipher past events can predict future patterns of virulence and transmission based on genetic signatures of adaptation and gene exchange. Both the effect of partial antimicrobial exposure and cell dormancy caused by variation in gene expression may accelerate the development of resistance. High-throughput sequencing can decode measurable evolution of cell populations within patients associated with systems-wide changes in gene expression during treatments. A multi-faceted approach can enhance assessment of antimicrobial resistance in E. coli ST131 by examining transmission dynamics between hosts to achieve a goal of pre-empting resistance before it emerges by optimising antimicrobial treatment protocols. PMID:27682088
Gaikwad, Satish; Kim, Ji-Ye; Lee, Hyun-Jeong; Jung, Suk Chan; Choi, Kang-Seuk
Domestic ducks are considered a potential reservoir of Newcastle disease virus. In the study, a Newcastle disease virus (NDV) isolated from a domestic duck during surveillance in South Korea was characterized. The complete genome of the NDV isolate was sequenced, and the phylogenetic relationship to reference strains was studied. Phylogenetic analysis revealed that the strain clustered in genotype I of Class II ND viruses, has highly phylogenetic similarity to NDV strains isolated from waterfowl in China, but was distant from the viruses isolated in chickens and vaccine strains used in South Korea. Pathogenicity experiment in chickens revealed it to be a lentogenic virus. The deduced amino acid sequence of the cleavage site of the fusion (F) protein confirmed that the isolate contained the avirulent motif (112)GKQGRL(117) at the cleavage site and caused no apparent disease in chickens and ducks. With phylogeographic analysis based on fusion gene, we estimate the origin of an ancestral virus of the isolate and its sister strain located in China around 1998. It highlights the need of continuous surveillance to enhance current understanding of the molecular epidemiology and evolution of the pathogenic strains.
Wang, Soon Joo; Choi, Jin Tae; Arnold, Jeffrey
South Korea has experienced > 30 suspected terrorism-related events since 1958, including attacks against South Korean citizens in foreign countries. The most common types of terrorism used have included bombings, shootings, hijackings, and kidnappings. Prior to 1990, North Korea was responsible for almost all terrorism-related events inside of South Korea, including multiple assassination attempts on its presidents, regular kidnappings of South Korean fisherman, and several high-profile bombings. Since 1990, most of the terrorist attacks against South Korean citizens have occurred abroad and have been related to the emerging worldwide pattern of terrorism by international terrorist organizations or deranged individuals. The 1988 Seoul Olympic Games provided a major stimulus for South Korea to develop a national emergency response system for terrorism-related events based on the participation of multiple ministries. The 11 September 2001 World Trade Center and Pentagon attacks and the 2001 United States of America (US) anthrax letter attacks prompted South Korea to organize a new national system of emergency response for terrorism-related events. The system is based on five divisions for the response to specific types of terrorist events, involving conventional terrorism, bioterrorism, chemical terrorism, radiological terrorism, and cyber-terrorism. No terrorism-related events occurred during the 2002 World Cup and Asian Games held in South Korea. The emergency management of terrorism-related events in South Korea is adapting to the changing risk of terrorism in the new century.
Kuller, Lewis H
Twenty-five years ago, on the 75th anniversary of the Johns Hopkins Bloomberg School of Public Health, I noted that epidemiologic research was moving away from the traditional approaches used to investigate "epidemics" and their close relationship with preventive medicine. Twenty-five years later, the role of epidemiology as an important contribution to human population research, preventive medicine, and public health is under substantial pressure because of the emphasis on "big data," phenomenology, and personalized medical therapies. Epidemiology is the study of epidemics. The primary role of epidemiology is to identify the epidemics and parameters of interest of host, agent, and environment and to generate and test hypotheses in search of causal pathways. Almost all diseases have a specific distribution in relation to time, place, and person and specific "causes" with high effect sizes. Epidemiology then uses such information to develop interventions and test (through clinical trials and natural experiments) their efficacy and effectiveness. Epidemiology is dependent on new technologies to evaluate improved measurements of host (genomics), epigenetics, identification of agents (metabolomics, proteomics), new technology to evaluate both physical and social environment, and modern methods of data collection. Epidemiology does poorly in studying anything other than epidemics and collections of numerators and denominators without specific hypotheses even with improved statistical methodologies.
Shin, Hyehyung; Yoon, Yeong Sook; Lee, Yoonna; Kim, Cho-il; Oh, Sang Woo
The objective of this study was to examine the relationship between dairy product intake and the incidence of metabolic syndrome (MetS) and its components among middle-aged Koreans. We examined 7,240 adults aged 40-69 yr without MetS at baseline over a 45.5-month follow-up period. They were taken from the Anseong and Ansan cohort of the Korean Genome and Epidemiology Study. Dairy product intake including milk, yogurt, and cheese was assessed with food frequency questionnaire. At the follow-up, the incidence of MetS was 17.1%. The incidences of MetS components were as follows: low HDL cholesterol (16.2%), abdominal obesity (14.0%), hypertriglyceridemia (13.8%), hyperglycemia (13.3%), and hypertension (13.1%). Adjusting for potential confounders, dairy product consumption frequency was inversely associated with the risk of MetS and abdominal obesity. Hazard ratio (HR) (95% confidence interval) for dairy product consumption more than 7 times/week compared to never was 0.75 (0.64-0.88, P for trend < 0.001) for MetS and 0.73 (0.61-0.88, P for trend < 0.001) for abdominal obesity. HR for milk intake was 0.79 for MetS and 0.82 for abdominal obesity. The results of this study suggest that daily intake of dairy products protects against the development of MetS, particularly abdominal obesity, in middle-aged Koreans.
Coutinho, Carla P.; dos Santos, Sandra C.; Madeira, Andreia; Mira, Nuno P.; Moreira, Ana S.; Sá-Correia, Isabel
Long-term respiratory infections with Burkholderia cepacia complex (Bcc) bacteria in cystic fibrosis (CF) patients generally lead to a more rapid decline in lung function and, in some cases, to a fatal necrotizing pneumonia known as the “cepacia syndrome.” Bcc bacteria are ubiquitous in the environment and are recognized as serious opportunistic pathogens that are virtually impossible to eradicate from the CF lung, posing a serious clinical threat. The epidemiological survey of Bcc bacteria involved in respiratory infections at the major Portuguese CF Treatment Center at Santa Maria Hospital, in Lisbon, has been carried out by our research group for the past 16 years, covering over 500 clinical isolates where B. cepacia and B. cenocepacia are the predominant species, with B. stabilis, B. contaminans, B. dolosa, and B. multivorans also represented. The systematic and longitudinal study of this CF population during such an extended period of time represents a unique case–study, comprehending 41 Bcc-infected patients (29 pediatric and 12 adult) of whom around 70% have been persistently colonized between 7 months and 9 years. During chronic infection, the CF airways represent an evolving ecosystem, with multiple phenotypic variants emerging from the clonal population and becoming established in the patients’ airways as the result of genetic adaptation. Understanding the evolutionary mechanisms involved is crucial for an improved therapeutic outcome of chronic infections in CF. This review focuses on our contribution to the understanding of these adaptive mechanisms based on extensive phenotypic, genotypic, and genome-wide expression approaches of selected Bcc clonal variants obtained during long-term colonization of the CF airways. PMID:22919578
Lee, Bo-Young; Shin, Dong Hyun; Cho, Seoae; Seo, Kang-Seok; Kim, Heebal
Many anthropometric measures, including body mass index (BMI), waist-to-hip ratio (WHR), and subcutaneous fat thickness, are used as indicators of nutritional status, fertility and predictors of future health outcomes. While BMI is currently the best available estimate of body adiposity, WHR and skinfold thickness at various sites (biceps, triceps, suprailiac, and subscapular) are used as indices of body fat distribution. Copy number variation (CNV) is an attractive emerging approach to the study of associations with various diseases. In this study, we investigated the dosage effect of genes in the CNV genome widely associated with fat distribution phenotypes in large cohorts. We used the Affymetrix genome-wide human SNP Array 5.0 data of 8,842 healthy unrelated adults in KARE cohorts and identified CNVs associated with BMI and fat distribution-related traits including WHR and subcutaneous skinfold thickness at suprailiac (SUP) and subscapular (SUB) sites. CNV segmentation of each chromosome was performed using Golden Helix SVS 7.0, and single regression analysis was used to identify CNVs associated with each phenotype. We found one CNV for BMI, 287 for WHR, 2,157 for SUP, and 2,102 for SUB at the 5% significance level after Holm-Bonferroni correction. Genes included in the CNV were used for the analysis of functional annotations using the Database for Annotation, Visualization and Integrated Discovery (DAVID v6.7b) tool. Functional gene classification analysis identified five significant gene clusters (metallothionein, ATP-binding proteins, ribosomal proteins, kinesin family members, and zinc finger proteins) for SUP, three (keratin-associated proteins, zinc finger proteins, keratins) for SUB, and one (protamines) for WHR. BMI was excluded from this analysis because the entire structure of no gene was identified in the CNV. Based on the analysis of genes enriched in the clusters, the fat distribution traits of KARE cohorts were related to the fat redistribution
Evaluation of a Phylogenetic Marker Based on Genomic Segment B of Infectious Bursal Disease Virus: Facilitating a Feasible Incorporation of this Segment to the Molecular Epidemiology Studies for this Viral Agent
Martínez-Pérez, Orlando; Dolz, Roser; Valle, Rosa; Perera, Carmen L.; Bertran, Kateri; Frías, Maria T.; Ganges, Llilianne; Díaz de Arce, Heidy; Majó, Natàlia; Núñez, José I.; Pérez, Lester J.
Background Infectious bursal disease (IBD) is a highly contagious and acute viral disease, which has caused high mortality rates in birds and considerable economic losses in different parts of the world for more than two decades and it still represents a considerable threat to poultry. The current study was designed to rigorously measure the reliability of a phylogenetic marker included into segment B. This marker can facilitate molecular epidemiology studies, incorporating this segment of the viral genome, to better explain the links between emergence, spreading and maintenance of the very virulent IBD virus (vvIBDV) strains worldwide. Methodology/Principal Findings Sequences of the segment B gene from IBDV strains isolated from diverse geographic locations were obtained from the GenBank Database; Cuban sequences were obtained in the current work. A phylogenetic marker named B-marker was assessed by different phylogenetic principles such as saturation of substitution, phylogenetic noise and high consistency. This last parameter is based on the ability of B-marker to reconstruct the same topology as the complete segment B of the viral genome. From the results obtained from B-marker, demographic history for both main lineages of IBDV regarding segment B was performed by Bayesian skyline plot analysis. Phylogenetic analysis for both segments of IBDV genome was also performed, revealing the presence of a natural reassortant strain with segment A from vvIBDV strains and segment B from non-vvIBDV strains within Cuban IBDV population. Conclusions/Significance This study contributes to a better understanding of the emergence of vvIBDV strains, describing molecular epidemiology of IBDV using the state-of-the-art methodology concerning phylogenetic reconstruction. This study also revealed the presence of a novel natural reassorted strain as possible manifest of change in the genetic structure and stability of the vvIBDV strains. Therefore, it highlights the need to obtain
Comparative population genomics of the Borrelia burgdorferi species complex reveals high degree of genetic isolation among species and underscores benefits and constraints to studying intra-specific epidemiological processes.
Jacquot, Maude; Gonnet, Mathieu; Ferquel, Elisabeth; Abrial, David; Claude, Alexandre; Gasqui, Patrick; Choumet, Valérie; Charras-Garrido, Myriam; Garnier, Martine; Faure, Benjamin; Sertour, Natacha; Dorr, Nelly; De Goër, Jocelyn; Vourc'h, Gwenaël; Bailly, Xavier
Lyme borreliosis, one of the most frequently contracted zoonotic diseases in the Northern Hemisphere, is caused by bacteria belonging to different genetic groups within the Borrelia burgdorferi species complex, which are transmitted by ticks among various wildlife reservoirs, such as small mammals and birds. These features make the Borrelia burgdorferi species complex an attractive biological model that can be used to study the diversification and the epidemiology of endemic bacterial pathogens. We investigated the potential of population genomic approaches to study these processes. Sixty-three strains belonging to three species within the Borrelia burgdorferi complex were isolated from questing ticks in Alsace (France), a region where Lyme disease is highly endemic. We first aimed to characterize the degree of genetic isolation among the species sampled. Phylogenetic and coalescent-based analyses revealed clear delineations: there was a ∼50 fold difference between intra-specific and inter-specific recombination rates. We then investigated whether the population genomic data contained information of epidemiological relevance. In phylogenies inferred using most of the genome, conspecific strains did not cluster in clades. These results raise questions about the relevance of different strategies when investigating pathogen epidemiology. For instance, here, both classical analytic approaches and phylodynamic simulations suggested that population sizes and migration rates were higher in B. garinii populations, which are normally associated with birds, than in B. burgdorferi s.s. populations. The phylogenetic analyses of the infection-related ospC gene and its flanking region provided additional support for this finding. Traces of recombination among the B. burgdorferi s.s. lineages and lineages associated with small mammals were found, suggesting that they shared the same hosts. Altogether, these results provide baseline evidence that can be used to formulate
Kim, Jinkwan; Lee, Seok Jun; Choi, Kyung-Mee; Lee, Seung Ku; Yoon, Dae Wui; Lee, Seung Gwan; Shin, Chol
Obstructive sleep apnea syndrome (OSA) has been recognized as a common health problem, and increasing obesity rates have led to further remarkable increases in the prevalence of OSA, along with more prominent cardiovascular morbidities. Though previous studies have reported an independent relationship between elevated high sensitivity C-reactive protein (hsCRP) levels and OSA, the issue remains controversial owing to inadequate consideration of obesity and various confounding factors. So far, few population based studies of association between OSA and hsCRP levels have been published. Therefore, the purpose of the present study was to investigate whether OSA is associated with increased hsCRP levels independent of obesity in a large population-based study. A total of 1,835 subjects (968 men and 867 women) were selected from a larger cohort of the ongoing Korean Genome and Epidemiology Study (KoGES). Overnight polysomnography was performed on each participant. All participants underwent anthropometric measurements and biochemical analyses, including analysis of lipid profiles and hsCRP levels. Based on anthropometric data, body mass index (BMI) and waist hip ratio (WHR) were calculated and fat mass (FM) were measured by means of multi-frequency bioelectrical impedance analysis (BIA). Mild OSA and moderate to severe OSA were defined by an AHI >5 and ≥15, respectively. The population was sub-divided into 3 groups based on the tertile cut-points for the distribution of hsCRP levels. The percentage of participants in the highest tertile of hsCRP increased dose-dependently according to the severity of OSA. After adjustment for potential confounders and obesity-related variables (BMI, WHR, and body fat) in a multiple logistic model, participants with moderate to severe OSA had 1.73-, 2.01-, and 1.61-fold greater risks of being in the highest tertile of hsCRP levels than participants with non-OSA, respectively. Interaction between obesity (BMI ≥25kg/m2) and the
Rhim, Jung Woo; Kim, Kyung Hyo; Kim, Dong Soo; Kim, Bong Seong; Kim, Jung Soo; Kim, Chang Hwi; Kim, Hwang Min; Park, Hee Ju; Pai, Ki Soo; Son, Byong Kwan; Shin, Kyung Sue; Oh, Moo Young; Woo, Young Jong; Yoo, Young; Lee, Kun Soo; Lee, Kyung Yil; Lee, Chong Guk; Lee, Joon Sung; Chung, Eun Hee; Choi, Eun Hwa; Hahn, Youn Soo; Park, Hyun Young; Kim, Joong Gon
This study represents the first epidemiological study based on the national registry of primary immunodeficiencies (PID) in Korea. Patient data were collected from 23 major hospitals. A total of 152 patients with PID (under 19 yr of age), who were observed from 2001 to 2005, have been entered in this registry. The period prevalence of PID in Korea in 2005 is 11.25 per million children. The following frequencies were found: antibody deficiencies, 53.3% (n = 81), phagocytic disorders, 28.9% (n = 44); combined immunodeficiencies, 13.2% (n = 20); and T cell deficiencies, 4.6% (n = 7). Congenital agammaglobulinemia (n = 21) and selective IgA deficiency (n = 21) were the most frequently reported antibody deficiency. Other reported deficiencies were common variable immunodeficiencies (n = 16), X-linked agammaglobulinemia (n = 15), IgG subclass deficiency (n = 4). Phagocytic disorder was mostly chronic granulomatous disease. A small number of patients with Wiskott-Aldrich syndrome, hyper-IgE syndrome, and severe combined immunodeficiency were also registered. Overall, the most common first manifestation was pneumonia. This study provides data that permit a more accurate estimation PID patients in Korea.
During the evolution of human immunodeficiency virus (HIV), transmissions between humans and primates resulted in multiple HIV lineages in humans. This evolution has been rapid, giving rise to a complex classification and allowing for worldwide spread and intermixing of subtypes, which has consequently led to dozens of circulating recombinant forms. In the Republic of Korea, 12,522 cases of HIV infection have been reported between 1985, when AIDS was first identified, and 2015. This review focuses on the evolution of HIV infection worldwide and the molecular epidemiologic characteristics of HIV in Korea. PMID:28332348
Overdiagnosis of thyroid cancer was propounded regarding the rapidly increasing incidence in South Korea. Overdiagnosis is defined as 'the detection of cancers that would never have been found were it not for the screening test', and may be an extreme form of lead bias due to indolent cancers, as is inevitable when conducting a cancer screening programme. Because it is solely an epidemiological concept, it can be estimated indirectly by phenomena such as a lack of compensatory drop in post-screening periods, or discrepancies between incidence and mortality. The erstwhile trials for quantifying the overdiagnosis in screening mammography were reviewed in order to secure the data needed to establish its prevalence in South Korea.
Lee, Hye-Eun; Kim, Hyoung Ryoul
Malignant mesothelioma and lung cancer are representative examples of occupational cancer. Lung cancer is the leading cause of cancer death, and the incidence of malignant mesothelioma is expected to increase sharply in the near future. Although information about lung carcinogen exposure is limited, it is estimated that the number of workers exposed to carcinogens has declined. The first official case of occupational cancer was malignant mesothelioma caused by asbestos exposure in the asbestos textile industry in 1992. Since then, compensation for occupational respiratory cancer has increased. The majority of compensated lung cancer was due to underlying pneumoconiosis. Other main causative agents of occupational lung cancer included asbestos, hexavalent chromium, and crystalline silica. Related jobs included welders, foundry workers, platers, plumbers, and vehicle maintenance workers. Compensated malignant mesotheliomas were associated with asbestos exposure. Epidemiologic studies conducted in Korea have indicated an elevated risk of lung cancer in pneumoconiosis patients, foundry workers, and asbestos textile workers. Occupational respiratory cancer has increased during the last 10 to 20 yr though carcinogen-exposed population has declined in the same period. More efforts to advance the systems for the investigation, prevention and management of occupational respiratory cancer are needed.
Despite a structured physical education system and related policies, dance education in Korea largely exists as a course in name only, without achieving its unique goals. It lacks standards within the physical education curriculum, which indicates that dance education is not conducted properly. Thus, the content and level of dance education vary…
This article describes two projects which Korea has undertaken to improve its school grounds: (1) the Green School Project; and (2) the School Forest Pilot Project. The Korean Ministry of Education and Human Resources Development (MOE&HRI) recently launched the Green School Project centred on existing urban schools with poor outdoor…
Kim, Soo Young; Lee, Yang Won; Choe, Yong Beom
Yeasts of the genus Malassezia are part of the normal flora of human skin. However, they are also associated with various skin diseases. Since the introduction of Malassezia to the Korean Dermatologic Society two decades ago, remarkable progress has been made in our knowledge of this genus. In this paper, we review recent developments in Malassezia research, including taxonomy and methods for species identification, recent genome analyses, Malassezia species distribution in healthy conditions and in specific skin diseases, trials investigating the mechanisms underlying Malassezia-related diseases, as well as therapeutic options. This review will enhance our understanding of Malassezia yeasts and related skin diseases in Korea. PMID:26719632
The Epidemiology and Genomics Research Program supports extramural research that investigates both genetic and environmental factors that may contribute to the etiology of cancer and/or impact cancer outcomes.
contusions, concussions, fractured skulls , ruptured occipital bones, facial lacerations, injuries to eyes and noses, and damaged blood vessels in the... Alienation "The principal reason the military cannot preside over a civilian government is that we officers have a strong tendency of confusing...KOREA socially alienated classes that could be potentially rebel- lious. Chong reacted by inviting the principals of the nation’s leading high
warfighting command in a doctrinally supporting relationship to the ROK armed forces. The evolution to a Korean -led defense of the Republic of Korea is a...T he Republic of Korea –U.S. alliance is embarking on the most profound transformation affecting American forces on the peninsula since the Korean ...War. For the last 57 years, the United States has led the war- fighting command responsible for the defense of the Republic of Korea (ROK). As the ROK
Jin, Sobeom; Hyun, Seung Gyu; Noh, Myunghyun
Significant tsunamis are described in historic and instrumental earthquake sources for all regions around the Korean Peninsula. According to the low seismicity near the Peninsula, there are relatively few tsunami events in Korea. Most of the tsunami events are associated with big earthquakes at the eastern margin of the East Sea. One historical event is associated with a volcanic eruption. For that reason, the eastern coast of the Korean Peninsula is the affectable area for tsunami. One historical event at the Yellow Sea area is inferred a result from a big earthquake in China. And one plate boundary earthquake between the Philippine Plate and the Eurasian Plate affected to an island located in south of the Korean Peninsula. We confirmed the historic tsunami events by review the foreign literatures. More detailed information is presented for the instrumental earthquake source events. This work was supported by the Nuclear Safety Research Program through the Korea Radiation Safety Foundation (KORSAFe) and the Nuclear Safety and Security Commission (NSSC), Republic of Korea (Grant No. 1305001).
Shahravan, Arash; Haghdoost, Ali Akbar
Epidemiology is the study of disease distribution and factors determining or affecting it. Likewise, endodontic epidemiology can be defined as the science of studying the distribution pattern and determinants of pulp and periapical diseases; specially apical periodontitis. Although different study designs have been used in endodontics, researchers must pay more attention to study designs with higher level of evidence such as randomized clinical trials. PMID:24688577
Park, Sanghun; Jung, Jihun; Oh, Seah; Jung, Hyowon; Oh, Younghee; Cho, Seokju; Cho, Seogju; Cho, Sungja; Park, Hyongsug; Jo, Namsook; Bae, Kyungwon; Choi, Sungmin; Kim, Bogsoon; Kim, Junghun; Chae, Youngzoo; Jung, Haesook; Cheon, Doosung; Kim, Hyunsoo
The present study has determined the detection rate of norovirus (NoV) with acute gastroenteritis (AGE) in hospitalized children and describes the molecular epidemiology of NoV circulating in Seoul, Korea. Six hundred and eighty-three (9.8%) of samples were positive for NoV. Of these, the NoV GII genogroup was the most commonly found, with a prevalence of 96.2% (683 of 710). Only 27 samples were positive for the NoV GI genogroup. Ten kinds of GI genotype (GI/1, GI/2, GI/3, GI/4, GI/5, GI/6, GI/7, GI/9, GI/12, and GI/13) and eight kinds of GII genotype (GII/2, GII/3, GII/4, GII/8, GII/14, GII/15, GII/16, and GII/17) were identified in children with AGE during the years 2008-2011.
Shaik, Sabiha; Kumar, Narender; Lankapalli, Aditya K.; Tiwari, Sumeet K.; Baddam, Ramani; Ahmed, Niyaz
A wide variety of genome sequencing platforms have emerged in the recent past. High-throughput platforms like Illumina and 454 are essentially adaptations of the shotgun approach generating millions of fragmented single or paired sequencing reads. To reconstruct whole genomes, the reads have to be assembled into contigs, which often require further downstream processing. The contigs can be directly ordered according to a reference, scaffolded based on paired read information, or assembled using a combination of the two approaches. While the reference-based approach appears to mask strain-specific information, scaffolding based on paired-end information suffers when repetitive elements longer than the size of the sequencing reads are present in the genome. Sequencing technologies that produce long reads can solve the problems associated with repetitive elements but are not necessarily easily available to researchers. The most common high-throughput technology currently used is the Illumina short read platform. To improve upon the shortcomings associated with the construction of draft genomes with Illumina paired-end sequencing, we developed Contig-Layout-Authenticator (CLA). The CLA pipeline can scaffold reference-sorted contigs based on paired reads, resulting in better assembled genomes. Moreover, CLA also hints at probable misassemblies and contaminations, for the users to cross-check before constructing the consensus draft. The CLA pipeline was designed and trained extensively on various bacterial genome datasets for the ordering and scaffolding of large repetitive contigs. The tool has been validated and compared favorably with other widely-used scaffolding and ordering tools using both simulated and real sequence datasets. CLA is a user friendly tool that requires a single command line input to generate ordered scaffolds. PMID:27248146
Shaik, Sabiha; Kumar, Narender; Lankapalli, Aditya K; Tiwari, Sumeet K; Baddam, Ramani; Ahmed, Niyaz
A wide variety of genome sequencing platforms have emerged in the recent past. High-throughput platforms like Illumina and 454 are essentially adaptations of the shotgun approach generating millions of fragmented single or paired sequencing reads. To reconstruct whole genomes, the reads have to be assembled into contigs, which often require further downstream processing. The contigs can be directly ordered according to a reference, scaffolded based on paired read information, or assembled using a combination of the two approaches. While the reference-based approach appears to mask strain-specific information, scaffolding based on paired-end information suffers when repetitive elements longer than the size of the sequencing reads are present in the genome. Sequencing technologies that produce long reads can solve the problems associated with repetitive elements but are not necessarily easily available to researchers. The most common high-throughput technology currently used is the Illumina short read platform. To improve upon the shortcomings associated with the construction of draft genomes with Illumina paired-end sequencing, we developed Contig-Layout-Authenticator (CLA). The CLA pipeline can scaffold reference-sorted contigs based on paired reads, resulting in better assembled genomes. Moreover, CLA also hints at probable misassemblies and contaminations, for the users to cross-check before constructing the consensus draft. The CLA pipeline was designed and trained extensively on various bacterial genome datasets for the ordering and scaffolding of large repetitive contigs. The tool has been validated and compared favorably with other widely-used scaffolding and ordering tools using both simulated and real sequence datasets. CLA is a user friendly tool that requires a single command line input to generate ordered scaffolds.
Kopfler, F.C.; Craun, G.F.
This volume is a compendium of peer-reviewed papers presented at the Symposium on Exposure Measurement and Evaluation Methods for Epidemiology, cosponsored in 1985 by the Health Effects Research Laboratory, USEPA, and the Division of Environmental Chemistry of the American Chemical Society. The book is divided into four sections: Use of Biological Monitoring to Assess Exposure, Epidemiologic Considerations for Assessing Exposure, Health and Exposure Data Bases, and Assessment of Exposure to Environmental Contaminants for Epidemiologic Studies. Both background papers and detailed reports of human studies are presented. The Biological Monitoring section contains reports of efforts to quantify adducts in blood and urine samples. In the section on Epidemiologic Considerations the feasibility of conducting epidemiologic studies of persons residing near hazardous waste sites and those exposed to arsenic in drinking water is described. The review of Data Bases includes government and industry water quality monitoring systems, the FDA Market Basket Study, major EPA air monitoring data, the National Database on Body Burden of Toxic chemicals, and the National Human Adipose Tissue Survey. Methods of assessing current exposure and estimating past exposure are detailed in the final section. Exposure to trichloroethylene in shower water, the relationship between water quality and cardiovascular disease, the contribution of environmental lead exposures to pediatric blood lead levels, and data from the TEAM study in which researchers compare indoor, outdoor, and breath analysis of air pollutant exposures are also discussed.
Palka, Eugene J., Ed.; Galgano, Francis A., Ed.
North Korea is a country about the size of the state of New York, inhabited by about 23 million people. It came into existence after the conclusion of World War II following decades of occupation of the Korean Peninsula by the Japanese empire. Dividing the peninsula into North and South Korea was the politically expedient solution to one of the…
The Moderate resolution Imaging Spectroradiometer (MODIS) on the Terra satellite detected several fires burning in South Korea on June 6, 2002. The smoke is blanketing both South and North Korea, and may be mingling with smoke from other fires in China. Beneath the haze, colored water at the southern tip of the Peninsula suggests sediment or phytoplankton in the coastal waters.
Escalera-Zamudio, Marina; Nelson, Martha I; Cobián Güemes, Ana Georgina; López-Martínez, Irma; Cruz-Ortiz, Natividad; Iguala-Vidales, Miguel; García, Elvia Rodríguez; Barrera-Badillo, Gisela; Díaz-Quiñonez, Jose Alberto; López, Susana; Arias, Carlos F; Isa, Pavel
In this work, nineteen influenza A/H3N2 viruses isolated in Mexico between 2003 and 2012 were studied. Our findings show that different human A/H3N2 viral lineages co-circulate within a same season and can also persist locally in between different influenza seasons, increasing the chance for genetic reassortment events. A novel minor cluster was also identified, named here as Korea, that circulated worldwide during 2003. Frequently, phylogenetic characterization did not correlate with the determined antigenic identity, supporting the need for the use of molecular evolutionary tools additionally to antigenic data for the surveillance and characterization of viral diversity during each flu season. This work represents the first long-term molecular epidemiology study of influenza A/H3N2 viruses in Mexico based on the complete genomic sequences and contributes to the monitoring of evolutionary trends of A/H3N2 influenza viruses within North and Central America.
Carbonari, Claudia Carolina; Fittipaldi, Nahuel; Teatero, Sarah; Athey, Taryn B T; Pianciola, Luis; Masana, Marcelo; Melano, Roberto G; Rivas, Marta; Chinen, Isabel
Shiga toxin-producing Escherichia coli strains are worldwide associated with sporadic human infections and outbreaks. In this work, we report the availability of high-quality draft whole-genome sequences for 19 O157:H7 strains isolated in Argentina.
Fittipaldi, Nahuel; Teatero, Sarah; Athey, Taryn B. T.; Pianciola, Luis; Masana, Marcelo; Melano, Roberto G.; Rivas, Marta; Chinen, Isabel
Shiga toxin-producing Escherichia coli strains are worldwide associated with sporadic human infections and outbreaks. In this work, we report the availability of high-quality draft whole-genome sequences for 19 O157:H7 strains isolated in Argentina. PMID:27908998
ABSTRACT Much of the genetic basis of complex traits is present on current genotyping products, but the individual variants that affect the traits have largely not been identified. Several traditional problems in genetic epidemiology have recently been addressed by assuming a polygenic basis for disease and treating it as a single entity. Here I briefly review some of these applications, which collectively may be termed polygenic epidemiology. Methodologies in this area include polygenic scoring, linear mixed models, and linkage disequilibrium scoring. They have been used to establish a polygenic effect, estimate genetic correlation between traits, estimate how many variants affect a trait, stratify cases into subphenotypes, predict individual disease risks, and infer causal effects using Mendelian randomization. Polygenic epidemiology will continue to yield useful applications even while much of the specific variation underlying complex traits remains undiscovered. PMID:27061411
Ostrom, Quinn T; Gittleman, Haley; Stetson, Lindsay; Virk, Selene M; Barnholtz-Sloan, Jill S
Gliomas are the most common type of primary intracranial tumors. Some glioma subtypes cause significant mortality and morbidity that are disproportionate to their relatively rare incidence. A very small proportion of glioma cases can be attributed to inherited genetic disorders. Many potential risk factors for glioma have been studied to date, but few provide explanation for the number of brain tumors identified. The most significant of these factors includes increased risk due to exposure to ionizing radiation, and decreased risk with history of allergy or atopic disease. The potential effect of exposure to cellular phones has been studied extensively, but the results remain inconclusive. Recent genomic analyses, using the genome-wide association study (GWAS) design, have identified several inherited risk variants that are associated with increased glioma risk. The following chapter provides an overview of the current state of research in the epidemiology of intracranial glioma.
... 15 Commerce and Foreign Trade 2 2010-01-01 2010-01-01 false North Korea. 746.4 Section 746.4... CONTROLS § 746.4 North Korea. (a) Licensing Requirements. As authorized by section 6 of the Export... Democratic People's Republic of Korea (North Korea), except food and medicines classified as...
Epidemiological methods, which combine population thinking and group comparisons, can primarily identify causes of disease in populations. There is therefore a tension between our intuitive notion of a cause, which we want to be deterministic and invariant at the individual level, and the epidemiological notion of causes, which are invariant only at the population level. Epidemiologists have given heretofore a pragmatic solution to this tension. Causal inference in epidemiology consists in checking the logical coherence of a causality statement and determining whether what has been found grossly contradicts what we think we already know: how strong is the association? Is there a dose-response relationship? Does the cause precede the effect? Is the effect biologically plausible? Etc. This approach to causal inference can be traced back to the English philosophers David Hume and John Stuart Mill. On the other hand, the mode of establishing causality, devised by Jakob Henle and Robert Koch, which has been fruitful in bacteriology, requires that in every instance the effect invariably follows the cause (e.g., inoculation of Koch bacillus and tuberculosis). This is incompatible with epidemiological causality which has to deal with probabilistic effects (e.g., smoking and lung cancer), and is therefore invariant only for the population.
Khang, Young-Ho; Lee, Sang-il
In recent years, health inequalities have become an important public health concern and the subject of both research and policy attention in Korea. Government reports, as well as many epidemiological studies, have provided evidence that a wide range of health outcomes and health-related behaviors are socioeconomically patterned, and that the magnitude of health inequalities is even increasing. However, except for the revised Health Plan 2010 targets for health equity, few government policies have explicitly addressed health inequalities. Although a number of economic and social policies may have had an impact on health inequalities, such impact has scarcely been evaluated. In this review, we describe the current status of research and policy on health inequalities in Korea. We also suggest future challenges of approaches and policies to reduce health inequalities and highlight the active and intensive engagement of many policy sectors and good evidence for interventions that will make meaningful reduction of health inequalities possible.
In recent years, health inequalities have become an important public health concern and the subject of both research and policy attention in Korea. Government reports, as well as many epidemiological studies, have provided evidence that a wide range of health outcomes and health-related behaviors are socioeconomically patterned, and that the magnitude of health inequalities is even increasing. However, except for the revised Health Plan 2010 targets for health equity, few government policies have explicitly addressed health inequalities. Although a number of economic and social policies may have had an impact on health inequalities, such impact has scarcely been evaluated. In this review, we describe the current status of research and policy on health inequalities in Korea. We also suggest future challenges of approaches and policies to reduce health inequalities and highlight the active and intensive engagement of many policy sectors and good evidence for interventions that will make meaningful reduction of health inequalities possible. PMID:22661869
Population Genomics and the Statistical Values of Race: An Interdisciplinary Perspective on the Biological Classification of Human Populations and Implications for Clinical Genetic Epidemiological Research
Maglo, Koffi N.; Mersha, Tesfaye B.; Martin, Lisa J.
The biological status and biomedical significance of the concept of race as applied to humans continue to be contentious issues despite the use of advanced statistical and clustering methods to determine continental ancestry. It is thus imperative for researchers to understand the limitations as well as potential uses of the concept of race in biology and biomedicine. This paper deals with the theoretical assumptions behind cluster analysis in human population genomics. Adopting an interdisciplinary approach, it demonstrates that the hypothesis that attributes the clustering of human populations to “frictional” effects of landform barriers at continental boundaries is empirically incoherent. It then contrasts the scientific status of the “cluster” and “cline” constructs in human population genomics, and shows how cluster may be instrumentally produced. It also shows how statistical values of race vindicate Darwin's argument that race is evolutionarily meaningless. Finally, the paper explains why, due to spatiotemporal parameters, evolutionary forces, and socio-cultural factors influencing population structure, continental ancestry may be pragmatically relevant to global and public health genomics. Overall, this work demonstrates that, from a biological systematic and evolutionary taxonomical perspective, human races/continental groups or clusters have no natural meaning or objective biological reality. In fact, the utility of racial categorizations in research and in clinics can be explained by spatiotemporal parameters, socio-cultural factors, and evolutionary forces affecting disease causation and treatment response. PMID:26925096
Ahn, Mi Young; Wertheim, Joel O; Kim, Woo Joo; Kim, Shin-Woo; Lee, Jin Soo; Ann, Hea Won; Jeon, Yongduk; Ahn, Jin Young; Song, Je Eun; Oh, Dong Hyun; Kim, Yong Chan; Kim, Eun Jin; Jung, In Young; Kim, Moo Hyun; Jeong, Wooyoung; Jeong, Su Jin; Ku, Nam Su; Kim, June Myung; Smith, Davey M; Choi, Jun Yong
Molecular epidemiology can help clarify the properties and dynamics of HIV-1 transmission networks in both global and regional scales. We studied 143 HIV-1-infected individuals recruited from four medical centers of three cities in South Korea between April 2013 and May 2014. HIV-1 env V3 sequence data were generated (337-793 bp) and analyzed using a pairwise distance-based clustering approach to infer putative transmission networks. Participants whose viruses were ≤2.0% divergent according to Tamura-Nei 93 genetic distance were defined as clustering. We collected demographic, risk, and clinical data and analyzed these data in relation to clustering. Among 143 participants, we identified nine putative transmission clusters of different sizes (range 2-4 participants). The reported risk factor of participants were concordant in only one network involving two participants, that is, both individuals reported homosexual sex as their risk factor. The participants in the other eight networks did not report concordant risk factors, although they were phylogenetically linked. About half of the participants refused to report their risk factor. Overall, molecular epidemiology provides more information to understand local transmission networks and the risks associated with these networks.
Ahn, Yeon-Soon; Jeong, Jae Sim
Occupational infection is a human disease caused by work-associated exposure to microbial agents through human and environmental contact. According to the literature, occupational infection was the third leading cause of occupational disease (861 cases, 8.0%), and health care, agricultural, forestry, and fishery workers were risk groups in Korea. In addition, most high-risk groups have not been protected by workers' compensation, which could lead to underestimation of the exact spectrum and magnitude of the problem, and may also result in a lack of development and implementation of occupational infection management. Through a review of national guidelines and documentations on prevention and control of occupational infection, a management strategy would promote adherence to worker safety regulations if it is explicit with regard to the agent and mode of infection in each of the high-risk groups. PMID:21258592
Kim, Kyoo Sang
Occupational asthma (OA) is the leading occupational respiratory disease. Cases compensated as OA by the Korea Workers' Compensation and Welfare Service (COMWEL) (218 cases), cases reported by a surveillance system (286 cases), case reports by related scientific journals and cases confirmed by the Occupational Safety and Health Research Institute (OSHRI) over 15 yr from 1992 to 2006 were analyzed. Annual mean incidence rate was 1.6 by compensation and 3.5 by surveillance system, respectively. The trend appeared to increase according to the surveillance system. Incidence was very low compared with other countries. The most frequently reported causative agent was isocyanate followed by reactive dye in dyeing factories. Other chemicals, metals and dust were also found as causative agents. OA was underreported according to compensation and surveillance system data. In conclusion, a more effective surveillance system is needed to evaluate OA causes and distribution, and to effectively prevent newly developing OA. PMID:21258586
Salathé, Marcel; Bengtsson, Linus; Bodnar, Todd J.; Brewer, Devon D.; Brownstein, John S.; Buckee, Caroline; Campbell, Ellsworth M.; Cattuto, Ciro; Khandelwal, Shashank; Mabry, Patricia L.; Vespignani, Alessandro
Mobile, social, real-time: the ongoing revolution in the way people communicate has given rise to a new kind of epidemiology. Digital data sources, when harnessed appropriately, can provide local and timely information about disease and health dynamics in populations around the world. The rapid, unprecedented increase in the availability of relevant data from various digital sources creates considerable technical and computational challenges. PMID:22844241
EPA, the Ministry of Environment of Korea, and partner agencies in both countries cooperate to strengthen environmental governance, improve air and water quality, and reduce exposure to toxic chemicals.
Song, Jing; Hu, Yonghua
Since the completion of the Human Genome Project in 2003 and the announcement of the Precision Medicine Initiative by U.S. President Barack Obama in January 2015, human beings have initially completed the " three steps" of " genomics to biology, genomics to health as well as genomics to society". As a new inter-discipline, the emergence and development of precision medicine have relied on the support and promotion from biological science, basic medicine, clinical medicine, epidemiology, statistics, sociology and information science, etc. Meanwhile, molecular epidemiology is considered to be the core power to promote precision medical as a cross discipline of epidemiology and molecular biology. This article is based on the characteristics and research progress of medicine and molecular epidemiology respectively, focusing on the contribution and significance of molecular epidemiology to precision medicine, and exploring the possible opportunities and challenges in the future.
Chin Se-ku. Yongbyon nuclear facility can be disabled within a year. JongAng Ilbo (internet version), March 13, 2007. 30 Abductions by N. Korea not...3007. 33 Choe Sang- hun and David E. Sanger, North Korea claims U.S. will remove sanctions, International Herald Tribune, September 4, 2007, p. 5...spring of 2007 to smuggle conventional arms, including machine guns , automatic rifles, and anti-tank rocket launchers, to the Tamil Tigers in Sri
Hong, Gye-Won; Won, Dong-Yeon; Kuk, Il-Hyun; Park, Jong-Chul
Superconductivity research in Korea was firstly carried out in the late 70's by a research group in Seoul National University (SNU), who fabricated a small scale superconducting magnetic energy storage system under the financial support from Korea Electric Power Company (KEPCO). But a few researchers were involved in superconductivity research until the oxide high Tc superconductor was discovered by Bednorz and Mueller. After the discovery of YBaCuO superconductor operating above the boiling point of liquid nitrogen (77 K)(exp 2), Korean Ministry of Science and Technology (MOST) sponsored a special fund for the high Tc superconductivity research to universities and national research institutes by recognizing its importance. Scientists engaged in this project organized 'High Temperature Superconductivity Research Association (HITSRA)' for effective conducting of research. Its major functions are to coordinate research activities on high Tc superconductivity and organize the workshop for active exchange of information. During last seven years the major superconductivity research has been carried out through the coordination of HITSRA. The major parts of the Korea's superconductivity research program were related to high temperature superconductor and only a few groups were carrying out research on conventional superconductor technology, and Korea Atomic Energy Research Institute (KAERI) and Korea Electrotechnology Research Institute (KERI) have led this research. In this talk, the current status and future plans of superconductivity research in Korea will be reviewed based on the results presented in interim meeting of HITSRA, April 1-2, 1994. Taejeon, as well as the research activity of KAERI.
Park, S. K.; Chung, U. S.; Jung, K. J.; Park, J. H.
Korea Research Reactor 1 (KRR-1), the first research reactor in Korea, has been operated since 1962, and the second one, Korea Research Reactor 2 (KRR-2) since 1972. The operation of both of them was phased out in 1995 due to their lifetime and operation of the new and more powerful research reactor, HANARO (High-flux Advanced Neutron Application Reactor; 30MW). Both are TRIGA Pool type reactors in which the cores are small self-contained units sitting in tanks filled with cooling water. The KRR-1 is a TRIGA Mark II, which could operate at a level of up to 250 kW. The second one, the KRR-2 is a TRIGA Mark III, which could operate at a level of up 2,000 kW. The decontamination and decommissioning (D & D) project of these two research reactors, the first D & D project in Korea, was started in January 1997 and will be completed to stage 3 by 2008. The aim of this decommissioning program is to decommission the KRR-1 & 2 reactors and to decontaminate the residual building structure s and the site to release them as unrestricted areas. KAERI (Korea Atomic Energy Research Institute) submitted the decommissioning plan and the environmental impact assessment reports to the Ministry of Science and Technology (MOST) for the license in December 1998, and was approved in November 2000.
Kwon, Hyuk Moo; Sung, Haan Woo; Meng, Xiang-Jin
Avian hepatitis E virus (avian HEV) is associated with hepatitis-splenomegaly (HS) syndrome or big liver and spleen disease in chickens. At least three genotypes of avian HEV have been identified from chickens worldwide. A total of 297 serum samples collected from chickens in 35 flocks in Korea were tested for avian HEV antibody with an enzyme-linked immunosorbent assay. The results showed that approximately 57 % of chicken flocks and 28 % of chickens from Korea were positive for antibodies to avian HEV. Thirteen pooled fecal samples from chickens were tested for avian HEV RNA by RT-PCR, and three fecal samples were positive. The partial helicase and capsid genes of the Korean avian HEV isolates were determined, and sequence analyses revealed that the Korean avian HEV isolates were clustered together and closely related to the genotype 1 avian HEV from Australia. The complete genomic sequence of a Korean avian HEV strain HH-F9 from a broiler breeder was determined, and shown to be 6,653 nt in length, excluding the poly (A) tail, which is 1 nt shorter than the prototype avian HEV from chicken with HS syndrome in the United States. Compared to the full-length sequences of other 5 known avian HEV strains worldwide, the Korean avian HEV shared approximately 83-97 % nucleotide sequence identity. The finding that Korean avian HEV belongs to genotype 1 avian HEV which was previously identified only from chickens in Australia has significant implication in understanding the global epidemiology of avian HEV.
Cai, X Q; Liu, G H; Song, H Q; Wu, C Y; Zou, F C; Yan, H K; Yuan, Z G; Lin, R Q; Zhu, X Q
Opisthorchis viverrini and Clonorchis sinensis are important trematodes infecting humans and animals, belonging to the family Opisthorchiidae. In the present study, we sequenced the nearly complete mitochondrial (mt) DNA (mtDNA) sequences of O. viverrini from Laos, obtained the complete mtDNA sequences of C. sinensis from China and Korea, and revealed their gene annotations and genome organizations. The mtDNA sequences of O. viverrini, C. sinensis (China isolate), C. sinensis (Korea isolate) were 13,510, 13,879, and 13,877 bp in size, respectively. Each of the three mt genomes comprises 36 genes, consisting of 12 genes coding for proteins, two genes for rRNA, and 20 genes (O. viverrini) or 22 genes (C. sinensis) for tRNA. The gene content and arrangement are identical to that of Fasciola hepatica, and Paragonimus westermani, but distinct from Schistosoma spp. All genes are transcribed in the same direction and have a nucleotide composition high in T. The contents of A + T of the mt genomes were 59.39% for O. viverrini, 60.03% for C. sinensis (China isolate), and 59.99% for C. sinensis (Korea isolate). Phylogenetic analyses using concatenated amino acid sequences of the 12 protein-coding genes, with three different computational algorithms [maximum parsimony, maximum likelihood, and Bayesian analysis], all revealed distinct groups with high statistical support, indicating that O. viverrini and C. sinensis represent sister taxa. These data provide additional novel mtDNA markers for studying the molecular epidemiology and population genetics of the two liver flukes and should have implications for the molecular diagnosis, prevention, and control of opisthorchiasis and clonorchiasis in humans and animals.
... Publications Birth Defects/ Child Health Cancer Cardiovascular Diseases Chronic Disease Ethics, Policy and Law Genomics in Practice Newborn Screening Pharmacogenomics Reproductive Health Tools/ Databases AMD Clips News Concepts/ Comments Pathogenicity/ Antimicrobial Resistance Epidemiology/ ...
Kim, Eun A
Korea has industrialized since the 1970s. Pneumoconiosis in coal miners was the most common occupational disease in the 1970s to 1980s. With the industrialization, the use of many chemicals have increased since the 1970s. As a consequence, there were outbreaks of occupational diseases caused by poisonous chemicals, such as heavy metal poisoning, solvent poisoning and occupational asthma in the late 1980s and early 1990s with civil movement for democracy. Many actions have been taken for prevention by the government, employers and employees or unions. In the 1990s most chemical related diseases and pneumoconiosis have rapidly decreased due to improving work environment. In the late 1990s, cerebro-cardiovascular diseases related to job stress or work overloads have abruptly increased especially after the economic crisis in 1998. After the year 2000, musculoskeletal disorders became a major problem especially in assembly lines in the manufacturing industry and they were expanded to the service industry. Mental diseases related to job stress have increased. Infectious diseases increased in health care workers and afforestation workers. Occupational cancers are increasing because of their long latency, although the use of carcinogenic substances are reduced, limited, and even banned. PMID:21258589
The dust cloud over eastern Asia was so thick on March 21, 2002, that the Korean Peninsula completely disappeared from view in this Sea-viewing Wide Field-of-view Sensor (SeaWiFS) image of the region. Parts of South Korea report that visibility at the surface is less than 50 m (165 feet). Airports throughout the region canceled flights due to the poor visibility. Eyewitnesses in China report that the dust was so thick in Beijing at times that visibility was limited to 100 m (330 feet), while in parts of the Gansu Province visibility was reported at less than 10 m (33 feet). Chinese officials say this is the worst dust storm to hit in more than 10 years. Dust from an earlier event still colors the air to the east of Japan. (The island of Honshu is just peeking out from under the cloud cover in these images.) Image courtesy the SeaWiFS Project, NASA/Goddard Space Flight Center, and ORBIMAGE
Karayiorgou, M.; Hwang, J.; Elango, R.
Our collaborative group has undertaken a linkage study of schizophrenia, using a systematic sample of patients admitted to Maryland hospitals. An initial sample of 39 families, each having two or more affecteds, was available for genotyping candidate genes, candidate regions, and highly polymorphic markers randomly distributed throughout the genome. We used a single complex dominant model (with a disease gene frequency of 0.005 and age-dependent penetrance for affected phenotype: for under 35, penetrance = .45; for 35 and older, penetrance = .85). We report here 130 markers which met the exclusion criteria of LOD score < -2.00 at theta > 0.01 in at least 10 informative families, and no evidence for heterogeneity. We also report here markers that were tested as candidates for linkage to the schizophrenic phenotype. They were selected based on the following criteria: (a) proximity to reported chromosomal rearrangements (both 5q and 11q), (b) suggestions of linkage from other families (5q), or (c) presence of a candidate gene (5q, 11q, 3q: dopamine receptors 1, 2, and 3, respectively). We also tested for mutations of codon 717 in exon 17 of the amyloid precursor protein (APP) gene and were unable to detect the C to T substitution in our schizophrenic group. 48 refs., 2 tabs.
Lee, Seung-Hun; Yun, Sun-Hee; Choi, Eunsang; Park, Yong-Soo; Lee, Sang-Eun; Cho, Gil-Jae; Kwon, Oh-Deog; Kwak, Dongmi
Lyme disease is a tick-borne zoonotic infectious disease caused by Borrelia burgdorferi. The present study assessed the infection status of B. burgdorferi among horses reared in Korea using ELISA and PCR. Between 2009 and 2013, blood samples were collected from 727 horses throughout Korea. Data for each animal including age, gender, breed, and region of sample collection were used for epidemiological analysis. Overall, 38 (5.2%; true prevalence: 5.5%) of 727 horses were seropositive by ELISA. There were statistically significant differences according to breed and region (P<0.001) whose differences might be attributed to the ecology of vector ticks and climate conditions. Using 2 nested PCR, none of the samples tested positive for B. burgdorferi. Thus, a positive ELISA result can indicate only that the tested horse was previously exposed to B. burgdorferi, with no certainty over the time of exposure. Since global warming is likely to increase the abundance of ticks in Korea, continuous monitoring of tick-borne diseases in Korean horses is needed. PMID:26951987
Lee, Seung-Hun; Yun, Sun-Hee; Choi, Eunsang; Park, Yong-Soo; Lee, Sang-Eun; Cho, Gil-Jae; Kwon, Oh-Deog; Kwak, Dongmi
Lyme disease is a tick-borne zoonotic infectious disease caused by Borrelia burgdorferi. The present study assessed the infection status of B. burgdorferi among horses reared in Korea using ELISA and PCR. Between 2009 and 2013, blood samples were collected from 727 horses throughout Korea. Data for each animal including age, gender, breed, and region of sample collection were used for epidemiological analysis. Overall, 38 (5.2%; true prevalence: 5.5%) of 727 horses were seropositive by ELISA. There were statistically significant differences according to breed and region (P<0.001) whose differences might be attributed to the ecology of vector ticks and climate conditions. Using 2 nested PCR, none of the samples tested positive for B. burgdorferi. Thus, a positive ELISA result can indicate only that the tested horse was previously exposed to B. burgdorferi, with no certainty over the time of exposure. Since global warming is likely to increase the abundance of ticks in Korea, continuous monitoring of tick-borne diseases in Korean horses is needed.
Hur, Jae-Seoun; Harada, Hiroshi; Oh, Soon-Ok; Lim, Kwang-Mi; Kang, Eui-Sung; Lee, Seung Mi; Kahng, Hyung-Yeel; Kim, Hyun-Woo; Jung, Jae-Sung; Koh, Young Jin
After an overview on the temporary situation of the lichenology in South Korea, localities of 95 macrolichen taxa are reported for South Korea. In this revised lichen flora of South Korea, 16 species are apparently new to the territory. Voucher specimens have been deposited in the Korean Lichen Research Institute (KoLRI) at Sunchon National University in Korea, and duplicates have also been donated to the National History Museum and Institute, in Chiba, (CBM) Japan.
Ali, Ibne Karim M.; Clark, C. Graham; Petri, William A.
Entamoeba histolytica, the causative agent of human amebiasis, remains a significant cause of morbidity and mortality in developing countries and is responsible for up to 100,000 deaths worldwide each year. Entamoeba dispar, morphologically indistinguishable from E. histolytica, is more common in humans in many parts of the world. Similarly Entamoeba moshkovskii, which was long considered to be a free-living ameba, is also morphologically identical to E. histolytica and E. dispar, and is highly prevalent in some E. histolytica endemic countries. However, the only species to cause disease in humans is E. histolytica. Most old epidemiological data on E. histolytica are unusable as the techniques employed do not differentiate between the above three Entamoeba species. Molecular tools are now available not only to diagnose these species accurately but also to study intra-species genetic diversity. Recent studies suggest that only a minority of all E. histolytica infections progress to development of clinical symptoms in the host and there exist population level differences between the E. histolytica strains isolated from the asymptomatic and symptomatic individuals. Nevertheless the underlying factors responsible for variable clinical outcome of infection by E. histolytica remain largely unknown. We anticipate that the recently completed E. histolytica genome sequence and new molecular techniques will rapidly advance our understanding of the epidemiology and pathogenicity of amebiasis. PMID:18571478
... Democratic People's Republic of Korea (North Korea), except food and medicines classified as EAR99... goods as described in this section to North Korea. (4) TSU for operation technology and software for lawfully exported commodities as set forth in § 740.13(a) and sales technology as set forth in § 740.13...
Kim, Byung Ha; Rhee, Kun Yong; Burns, Carol; Lerner, Janet W.
Daegu University has enjoyed a long and remarkable history of special education. Daegu University is large University located in Daegu, South Korea, a large city in South Korea that is south of Seoul. Since the 1970's, South Korea has achieved unusual and comprehensive growth in its economy, and the field of special education continued to thrive…
... Part 510 North Korea Sanctions Regulations AGENCY: Office of Foreign Assets Control, Treasury. ACTION... amending the North Korea Sanctions Regulations to implement Executive Order 13570 of April 18, 2011. OFAC..., the Department of the Treasury's Office of Foreign Assets Control published the North Korea...
Cha, Eun Shil; Jeong, Mihye; Lee, Won Jin
This study aims to review agricultural pesticide usage and trends and to identify hazardous pesticides for regulation, in terms of public health, in South Korea. The authors collected data on usage and trends of agricultural pesticides through agriculture-related databases. Criteria from the US Environmental Protection Agency classification for carcinogenicity, World Health Organization classification for acute toxicity, and European Union prioritization list for endocrine-disrupting chemicals were used for the hazard categorization of identified individual active ingredients. Pesticides to be prioritized among all pesticides used in South Korea between 2007 and 2011 were selected by taking into account the volume of usage, toxicity, and epidemiological evidence. Annual agricultural use of pesticides has increased rapidly from the 1970s to 1990s in South Korea, but has declined since 2001. The quantity of pesticides used in 2011 was reported as 19,131 tons, and was comprised of 34.7% insecticides, 28.0% fungicides, and 27.1% herbicides. The 50 pesticides with the greatest volume of usage accounted for 82.6% of the total volume of pesticides used between 2007 and 2011, with the most-used active ingredient being machine oil, followed by mancozeb and then paraquat. Organophosphates were the most used among the top 50 pesticides. A total of 24 pesticides were selected for recommendation of intensive regulation in South Korea. In conclusion, the authors described the usage and trends of overall agricultural pesticides, which would serve as a fundamental step forward in managing pesticide in terms of public health. Intensive efforts are required for the prevention of potential health effects from the 24 identified pesticides.
Kang, Eunjeong; Lee, Youngsoo; Harris, Patrick; Koh, Kwangwook; Kim, Keonyeop
Recently, Health Impact Assessment has gained great attention in Korea. First, the Ministry of Environment introduced HIA within existing Environment Impact Assessment. Second, the Korea Institute for Health and Social Affairs began an HIA program in 2008 in alliance with Healthy Cities. In this short report, these two different efforts are introduced and their opportunities and challenges discussed. We believe these two approaches complement each other and both need to be strengthened. We also believe that both can contribute to the development of health in policy and project development and ultimately to improvements in the Korean population's health.
Ahn, Yeon-Soon; Kang, Seong-Kyu
Compensation for asbestos-related cancers occurring in occupationally-exposed workers is a global issue; this is also an issue in Korea. To provide basic information regarding compensation for workers exposed to asbestos, 60 cases of asbestos-related occupational lung cancer and mesothelioma that were compensated during 15 yr; from 1993 (the year the first case was compensated) to 2007 by the Korea Labor Welfare Corporation (KLWC) are described. The characteristics of the cases were analyzed using the KLWC electronic data and the epidemiologic investigation data conducted by the Occupational Safety and Health Research Institute (OSHRI) of the Korea Occupational Safety and Health Agency (KOSHA). The KLWC approved compensation for 41 cases of lung cancer and 19 cases of mesothelioma. Males accounted for 91.7% (55 cases) of the approved cases. The most common age group was 50-59 yr (45.0%). The mean duration of asbestos exposure for lung cancer and mesothelioma cases was 19.2 and 16.0 yr, respectively. The mean latency period for lung cancer and mesothelioma cases was 22.1 and 22.6 yr, respectively. The major industries associated with mesothelioma cases were shipbuilding and maintenance (4 cases) and manufacture of asbestos textiles (3 cases). The major industries associated with lung cancer cases were shipbuilding and maintenance (7 cases), construction (6 cases), and manufacture of basic metals (4 cases). The statistics pertaining to asbestos-related occupational cancers in Korea differ from other developed countries in that more cases of mesothelioma were compensated than lung cancer cases. Also, the mean latency period for disease onset was shorter than reported by existing epidemiologic studies; this discrepancy may be related to the short history of occupational asbestos use in Korea. Considering the current Korean use of asbestos, the number of compensated cases in Korea is expected to increase in the future but not as much as developed countries.
Genome-Wide Linkage Screen for Systolic Blood Pressure in the Veterans Administration Genetic Epidemiology Study (VAGES) of Mexican-Americans and Confirmation of a Major Susceptibility Locus on Chromosome 6q14.1
Puppala, Sobha; Coletta, Dawn K.; Schneider, Jennifer; Hu, Shirley L.; Farook, Vidya S.; Dyer, Thomas D.; Arya, Rector; Blangero, John; Duggirala, Ravindranath; DeFronzo, Ralph A.; Jenkinson, Christopher P.
Objective Hypertension or high blood pressure is a strong correlate of diseases such as obesity and type 2 diabetes. We conducted a genome-wide linkage screen to identify susceptibility genes influencing systolic blood pressure (SBP) and diastolic blood pressure (DBP) in Mexican-Americans from the Veterans Administration Genetic Epidemiology Study (VAGES). Methods Using data from 1,089 individuals distributed across 266 families, we performed a multipoint linkage analysis to localize susceptibility loci for SBP and DBP by applying two models. In model 1, we added a sensible constant to the observed BP values in treated subjects [Tobin et al.; Stat Med 2005;24:2911–2935] to account for antihypertensive use (i.e. 15 and 10 mm Hg to SBP and DBP values, respectively). In model 2, we fixed values of 140 mm Hg for SBP and 90 mm Hg for DBP, if the treated values were less than the standard referenced treatment thresholds of 140/90 mm Hg for hypertensive status. However, if the observed treated BP values were found to be above these standard treatment thresholds, the actual observed treated BP values were retained in order not to reduce them by substitution of the treatment threshold values. Results The multipoint linkage analysis revealed strong linkage signals for SBP compared with DBP. The strongest evidence for linkage of SBP (model 1, LOD = 5.0; model 2, LOD = 3.6) was found on chromosome 6q14.1 near the marker D6S1031 (89 cM) in both models. In addition, some evidence for SBP linkage occurred on chromosomes 1q, 4p, and 16p. Most importantly, our major SBP linkage finding on chromosome 6q near marker D6S1031 was independently confirmed in a Caucasian population (LOD = 3.3). In summary, our study found evidence for a major locus on chromosome 6q influencing SBP levels in Mexican-Americans. PMID:21293138
Kim, Dasom; Kim, Jihye
This cohort study examined the association between total and individual dairy products and the risk of developing the metabolic syndrome (MetS) and its components in Korean adults from the Korean Genome and Epidemiology Study. We prospectively analysed 5510 participants aged 40-69 years without the MetS at baseline during a 10-year follow-up period. Dairy consumption was assessed with a semi-quantitative FFQ at baseline and after 4 years. The MetS was defined according to the criteria by the National Cholesterol Education Program Adult Treatment Panel III. The Cox's proportional hazard model was used to examine the association between consumption of total dairy products, milk and yogurt in servings per week and the risk of incident MetS or individual components. A total of 2103 subjects developed the MetS (38·2 %) during an average follow-up of 67·4 months (range 17-104 months). Frequent dairy consumption (>7 servings of total dairy and milk/week, ≥4 servings of yogurt/week) was associated with a reduced risk of incident MetS and its components. In the multivariable adjusted model, hazard ratios for the MetS were 0·51 (95 % CI 0·43, 0·61) for total dairy products, 0·50 (95 % CI 0·38, 0·66) for milk and 0·67 (95 % CI 0·57, 0·78) for yogurt in frequent consumers compared with non-consumers. An inverse association between milk/yogurt and low HDL-cholesterol was shown only in women. In conclusion, high consumption of individual dairy products including milk and yogurt as well as total dairy were associated with a reduced risk of incident MetS and individual components in Korean adults.
Lee, Seung-Ho; Kim, Won-Keun; No, Jin Sun; Kim, Jeong-Ah; Kim, Jin Il; Gu, Se Hun; Kim, Heung-Chul; Klein, Terry A.; Park, Man-Seong; Song, Jin-Won
Hantaviruses (family Bunyaviridae) are enveloped negative-sense tripartite RNA viruses. The natural hosts of hantaviruses include rodents, shrews, moles, and bats. Imjin virus (MJNV) is a shrew-borne hantavirus identified from the Ussuri white-toothed shrews (Crocidura lasiura) in the Republic of Korea (ROK) and China. We have isolated MJNV and determined its prevalence and molecular diversity in Gyeonggi province, ROK. However, the distribution and phylogeography of MJNV in other regions of ROK remain unknown. A total of 96 C. lasiura were captured from Gangwon and Gyeonggi provinces, ROK, during 2011–2014. Among them, four (4.2%) shrews were positive for anti-MJNV IgG and MJNV RNA was detected from nine (9.4%), respectively. Based on the prevalence of MJNV RNA, the preponderance of infected shrews was male and adult, consistent with the gender- and weight-specific prevalence of hantaviruses in other species. We monitored the viral load of MJNV RNA in various tissues of shrews, which would reflect the dynamic infectious status and circulation of MJNV in nature. Our phylogeographic and genomic characterization of MJNV suggested natural occurrences of recombination and reassortment in the virus population. Thus, these findings provide significant insights into the epidemiology, phylogeographic diversity, and dynamic circulation and evolution of shrew-borne hantaviruses. PMID:28295052
Park, Hyun-Seok; Kang, Myong-Jin
Objective Rapid increase in aged population and westernization of lifestyle have modified epidemiological status of stroke. The purpose of this study is to analyze changing trends of stroke epidemiology in South Korea. Methods We reviewed retrospectively medical records of 1,124 cases diagnosed as stroke among 54,534 patients who visited the Emergency Medical Center at our hospital from January 1994 to December 1996 (Group A). Also, we evaluated 1,705 cases diagnosed as stroke among 55,381 patients who visited to the same hospital from January 2003 to December 2005 (Group B). The variable features of stroke, such as age, sex, seasonal variation and distribution of stroke subtypes were studied by comparing group A with B. Results In group A, hemorrhagic stroke (67.9%) was more prevalent than ischemic stroke (32.1%). However, group B showed that the ratio of hemorrhagic stroke (40.3%) to ischemic stroke (59.6%) has been reversed. The highest incidence of stroke was noted in their sixties and seventies of age in group B, which was older than that of group A. In group A, male ischemic stroke (IS) patients outnumbered female patients (1.26:1). Moreover, this gender disproportion became higher in group B (1.53:1). In group A, the number of male intracerebral hermorrhage (ICH) patients were similar to that of female patients (0.97:1). However, male ICH patients outnumbered female patients in group B (1.23:1). As for subarachnoid hemorrhage (SAH), female patients outnumbered male patients more than two-fold in both groups. Both groups showed that the occurrence of ischemic stroke was highest in summer, but that of hemorrhagic stroke was the highest in winter. Conclusion This study showed the changing trends of stroke in its distribution of subtypes. Multicenter prospective study using stroke registry would be required for the determination of national epidemiologic trends. PMID:19096539
Cho, H G; Lee, S G; Kim, W H; Lee, J S; Park, P H; Cheon, D S; Jheong, W H; Jho, E H; Lee, J B; Paik, S Y
Epidemiological and virological studies indicate that noroviruses-contaminated groundwater was the primary source of four acute gastroenteritis outbreaks in South Korea between 2008 and 2012. Furthermore, cabbage kimchi was first identified as the vehicle of transmission between groundwater and infected patients in an outbreak in 2011. The proper treatment of groundwater sources prior to use for drinking or in food preparation is necessary to prevent further outbreaks.
Characterizes the past 40 years in South Korea as a time of modernization, industrialization, urbanization, and internationalization. Discusses Korean religion and social values; family, kinship, and social life; education; housing, food, and clothing; leisure and sports; and the maintenance of national identity. Examines the Korean synthesis of…
The purpose of this paper is to examine the current implementation of inclusive education in South Korea and discuss its challenges. The history of special education is first described followed by an introduction to policies relevant to special and inclusive education. Next, a critical discussion of the state of inclusive education follows built…
Brandt, Vincent S. R.
Reviews development in rural areas of South Korea since the late nineteenth century, with particular emphasis on rural to urban migration, governmental investment in agriculture, transportation and mass communications, development projects, social leveling processes, upgraded living standards, and cooperative village improvement projects. Journal…
Baek, Myung-Jin; Kim, Zeen-Chul
via Korea Aerospace Research Institute (KARI) as the prime contractor in the area of Korea earth observation satellite program to enhance Korea's space program development capability. In this paper, Korea's on-going and future earth observation satellite programs are introduced: KOMPSAT- 1 (Korea Multi Purpose Satellite-1), KOMPSAT-2 and Communication, Broadcasting and Meteorological Satellite (CBMS) program. KOMPSAT-1 satellite successfully launched in December 1999 with Taurus launch vehicle. Since launch, KOMPSAT-1 is downlinking images of Korea Peninsular every day. Until now, KOMPSAT-1 has been operated more than 2 and half years without any major hardware malfunction for the mission operation. KOMPSAT-1 payload has 6.6m panchromatic spatial resolution at 685 km on-orbit and the spacecraft bus had NASA TOMS-EP (Total Ozone Mapping Spectrometer-Earth Probe) spacecraft bus heritage designed and built by TRW, U.S.A.KOMPSAT-1 program was international co-development program between KARI and TRW funded by Korean Government. be launched in 2004. Main mission objective is to provide geo-information products based on the multi-spectral high resolution sensor called Multi-Spectral Camera (MSC) which will provide 1m panchromatic and 4m multi-spectral high resolution images. ELOP of Israel is the prime contractor of the MSC payload system and KARI is the total system prime contractor including spacecraft bus development and ground segment. KARI also has the contract with Astrium of Europe for the purpose of technical consultation and hardware procurement. Based on the experience throughout KOMPSAT-1 and KOMPSAT-2 space system development, Korea is expecting to establish the infrastructure of developing satellite system. Currently, KOMPSAT-2 program is in the critical design stage. are scheduled to launch in 2008 and in 2014, respectively. The mission of CBMS consists of two areas. One is of space technology test for the communications mission, and the other is of a real
Lee, Sukyee; Lee, Seung-Hun; VanBik, Dorene; Kim, Neung-Hee; Kim, Kyoo-Tae; Goo, Youn-Kyoung; Rhee, Man Hee; Kwon, Oh-Deog; Kwak, Dongmi
In this study, the status of Anaplasma phagocytophilum infection was assessed in shelter dogs in Seoul, Korea, with PCR and phylogenetic analyses. Nested PCR on 1058 collected blood samples revealed only one A. phagocytophilum positive sample (female, age <1year, mixed breed, collected from the north of the Han River). The genetic variability of A. phagocytophilum was evaluated by genotyping, using the 16S rRNA, groEL, and msp2 gene sequences of the positive sample. BLASTn analysis revealed that the 16S rRNA, groEL, and msp2 genes had 99.6%, 99.9%, and 100% identity with the following sequences deposited in GenBank: a cat 16S rRNA sequence from Korea (KR021166), a rat groEL sequence from Korea (KT220194), and a water deer msp2 sequence from Korea (HM752099), respectively. Phylogenetic analyses classified the groEL gene into two distinct groups (serine and alanine), whereas the msp2 gene showed a general classification into two groups (USA and Europe) that were further subgrouped according to region. To the best of our knowledge, this study is the first to describe the molecular diagnosis of A. phagocytophilum in dogs reared in Korea. In addition, the high genetic identity of the 16S rRNA and groEL sequences between humans and dogs from the same region suggests a possible epidemiological relation. Given the conditions of climate change, tick ecology, and recent incidence of human granulocytic anaplasmosis in Korea, the findings of this study underscore the need to establish appropriate control programs for tick-borne diseases in Korea.
Park, Ji-Sun; Lee, Sung-Geun; Jin, Ji-Young; Cho, Han-Gil; Jheong, Weon-Hwa; Paik, Soon-Young
Norovirus is the primary cause of acute gastroenteritis in individuals of all ages. In Australia, a new strain of norovirus (GII.4) was identified in March 2012, and this strain has spread rapidly around the world. In August 2012, this new GII.4 strain was identified in patients in South Korea. Therefore, to examine the characteristics of the epidemic norovirus GII.4 2012 variant in South Korea, we conducted KM272334 full-length genomic analysis. The genome of the gg-12-08-04 strain consisted of 7,558 bp and contained three open reading frame (ORF) composites throughout the whole genome: ORF1 (5,100 bp), ORF2 (1,623 bp), and ORF3 (807 bp). Phylogenetic analyses showed that gg-12-08-04 belonged to the GII.4 Sydney 2012 variant, sharing 98.92% nucleotide similarity with this variant strain. According to SimPlot analysis, the gg-12-08-04 strain was a recombinant strain with breakpoint at the ORF1/2 junction between Osaka 2007 and Apeldoorn 2008 strains. This study is the first report of the complete sequence of the GII.4 Sydney 2012 strain in South Korea. Therefore, this may represent the standard sequence of the norovirus GII.4 2012 variant in South Korea and could therefore be useful for the development of norovirus vaccines.
Ahn, Song Vogue; Kwon, Sung Won
Purpose We aimed to evaluate obesity, a risk factor of metabolic syndrome, and its association with prostatic enlargement in a retrospective cohort in Korea. Methods Baseline data were obtained from the Korean Genome and Epidemiology Study on Atherosclerosis Risk of Rural Areas in the Korean General Population (KoGES-ARIRANG). Between March 2015 and November 2015, 2,127 male participants of KoGES-ARIRANG were invited to the Korean Prostate Health Council Screening Program, and 602 participants underwent urological examination, including serum prostate specific antigen measurement and transrectal ultrasonography, and completed the International Prostate Symptom Score questionnaire. The data for 571 participants were analyzed, after excluding 31 men who had a history of prostatic disease or testosterone replacement, or had undergone a prior prostatic surgery or procedure. Results Among components of metabolic syndrome, waist circumference had a statistically significant linear correlation with incremental increases in prostate volume (B=0.181, P=0.004). Abdominal obesity as determined by anthropometric measures including body mass index (odds ratio [OR], 1.205; 95% confidence interval [CI], 1.088–1.336), waist circumference (OR, 1.073; 95% CI, 1.032–1.115), body fat (OR, 1.126; 95% CI, 1.056–1.202), and visceral fat composition (OR, 1.667; 95% CI, 1.246–2.232) was significantly associated with the presence of high-volume benign prostatic hyperplasia (BPH) (prostate volume≥ 40 mL). Furthermore, the highest quartile of serum leptin (OR, 3.541; 95% CI, 1.103–11.365) and adiponectin levels (OR, 0.315; 95% CI, 0.102–0.971) were significantly correlated with high-volume BPH compared to the lowest quartile of levels. Conclusions Abdominal obesity and serum leptin level are positively associated with prostate growth, whereas serum adiponectin level is inversely associated with the presence of prostatic enlargement. PMID:28043110
Cha, S-Y; Kang, M; Cho, J-G; Jang, H-K
The genetic organization of the 24 duck circovirus (DuCV) strains detected in commercial Pekin ducks from South Korea between 2011 and 2012 is described in this study. Multiple sequence alignment and phylogenetic analyses were performed on the 24 viral genome sequences as well as on 45 genome sequences available from the GenBank database. Phylogenetic analyses based on the genomic and open reading frame 2/cap sequences demonstrated that all DuCV strains belonged to genotype 1 and were designated in a subcluster under genotype 1. Analysis of the capsid protein amino acid sequences of the 24 Korean DuCV strains showed 10 substitutions compared with that of other genotype 1 strains. Our analysis showed that genotype 1 is predominant and circulating in South Korea. These present results serve as incentive to add more data to the DuCV database and provide insight to conduct further intensive study on the geographic relationships among these virus strains.
Interaction of methylation-related genetic variants with circulating fatty acids on plasma lipids: a meta-analysis of 7 studies and methylation analysis of 3 studies in the Cohorts for Heart and Aging Research in Genomic Epidemiology consortium12
Follis, Jack L; Smith, Caren E; Tanaka, Toshiko; Manichaikul, Ani W; Chu, Audrey Y; Samieri, Cecilia; Zhou, Xia; Guan, Weihua; Wang, Lu; Biggs, Mary L; Chen, Yii-Der I; Hernandez, Dena G; Borecki, Ingrid; Chasman, Daniel I; Rich, Stephen S; Ferrucci, Luigi; Irvin, Marguerite Ryan; Aslibekyan, Stella; Zhi, Degui; Tiwari, Hemant K; Claas, Steven A; Sha, Jin; Kabagambe, Edmond K; Lai, Chao-Qiang; Parnell, Laurence D; Lee, Yu-Chi; Amouyel, Philippe; Lambert, Jean-Charles; Psaty, Bruce M; King, Irena B; Mozaffarian, Dariush; McKnight, Barbara; Bandinelli, Stefania; Tsai, Michael Y; Ridker, Paul M; Ding, Jingzhong; Mstat, Kurt Lohmant; Liu, Yongmei; Sotoodehnia, Nona; Barberger-Gateau, Pascale; Steffen, Lyn M; Siscovick, David S; Absher, Devin; Arnett, Donna K; Ordovás, José M; Lemaitre, Rozenn N
Background: DNA methylation is influenced by diet and single nucleotide polymorphisms (SNPs), and methylation modulates gene expression. Objective: We aimed to explore whether the gene-by-diet interactions on blood lipids act through DNA methylation. Design: We selected 7 SNPs on the basis of predicted relations in fatty acids, methylation, and lipids. We conducted a meta-analysis and a methylation and mediation analysis with the use of data from the CHARGE (Cohorts for Heart and Aging Research in Genomic Epidemiology) consortium and the ENCODE (Encyclopedia of DNA Elements) consortium. Results: On the basis of the meta-analysis of 7 cohorts in the CHARGE consortium, higher plasma HDL cholesterol was associated with fewer C alleles at ATP-binding cassette subfamily A member 1 (ABCA1) rs2246293 (β = −0.6 mg/dL, P = 0.015) and higher circulating eicosapentaenoic acid (EPA) (β = 3.87 mg/dL, P = 5.62 × 1021). The difference in HDL cholesterol associated with higher circulating EPA was dependent on genotypes at rs2246293, and it was greater for each additional C allele (β = 1.69 mg/dL, P = 0.006). In the GOLDN (Genetics of Lipid Lowering Drugs and Diet Network) study, higher ABCA1 promoter cg14019050 methylation was associated with more C alleles at rs2246293 (β = 8.84%, P = 3.51 × 1018) and lower circulating EPA (β = −1.46%, P = 0.009), and the mean difference in methylation of cg14019050 that was associated with higher EPA was smaller with each additional C allele of rs2246293 (β = −2.83%, P = 0.007). Higher ABCA1 cg14019050 methylation was correlated with lower ABCA1 expression (r = −0.61, P = 0.009) in the ENCODE consortium and lower plasma HDL cholesterol in the GOLDN study (r = −0.12, P = 0.0002). An additional mediation analysis was meta-analyzed across the GOLDN study, Cardiovascular Health Study, and the Multi-Ethnic Study of Atherosclerosis. Compared with the model without the adjustment of cg14019050 methylation, the model with such
Second- 28 Yi Sang-il and Chin Se-ku. Yongbyon nuclear facility can be disabled within...The White House, Roundtable Interview of the President by Foreign Print Media, August 30, 3007. 32 Choe Sang- hun and David E. Sanger, North Korea...2006 through the spring of 2007 to smuggle conventional arms, including machine guns , automatic rifles, and anti-tank rocket launchers, to the
and Chin Se-ku. Yongbyon nuclear facility can be disabled within a year. JongAng Ilbo (internet version), March 13, 2007. Korea’s nuclear programs and...the President by Foreign Print Media, August 30, 3007. 30 Choe Sang- hun and David E. Sanger, North Korea claims U.S. will remove sanctions...including machine guns , automatic rifles, and anti-tank rocket launchers, to the Tamil Tigers in Sri Lanka. The Sri Lankan navy intercepted and
News , December 1, 2012. U.S.- South Korea Relations Congressional Research Service 7 • China’s rising influence in ...entered into force and will be eliminated completely in the fifth year of the agreement. South Korea also agreed to allow U.S.-based car manufacturers to...sell in South Korea up to 25,000 cars per year per manufacturer as long as they met U.S. safety and environmental standards. This
Choi, Seong Jin; Park, Sang-Won; Bae, In-Gyu; Kim, Sung-Han; Ryu, Seong Yeol; Kim, Hyun Ah; Jang, Hee-Chang; Hur, Jian; Jun, Jae-Bum; Jung, Younghee; Chang, Hyun-Ha; Kim, Young Keun; Yi, Jongyoun; Kim, Kye-Hyung; Hwang, Jeong-Hwan; Kim, Yeon-Sook; Jeong, Hye Won; Song, Kyoung-Ho; Park, Wan Beom; Kim, Eu Suk; Oh, Myoung-don
Background Severe fever with thrombocytopenia syndrome (SFTS) is an emerging infectious disease that was recently identified in China, South Korea and Japan. The objective of the study was to evaluate the epidemiologic and clinical characteristics of SFTS in South Korea. Methods/Principal Findings SFTS is a reportable disease in South Korea. We included all SFTS cases reported to the Korea Centers for Disease Control and Prevention (KCDC) from January 2013 to December 2015. Clinical information was gathered by reviewing medical records, and epidemiologic characteristics were analyzed using both KCDC surveillance data and patient medical records. Risk factors for mortality in patients with SFTS were assessed. A total of 172 SFTS cases were reported during the study period. SFTS occurred throughout the country, except in urban areas. Hilly areas in the eastern and southeastern regions and Jeju island (incidence, 1.26 cases /105 person-years) were the main endemic areas. The yearly incidence increased from 36 cases in 2013 to 81 cases in 2015. Most cases occurred from May to October. The overall case fatality ratio was 32.6%. The clinical progression was similar to the 3 phases reported in China: fever, multi-organ dysfunction, and convalescence. Confusion, elevated C-reactive protein, and prolonged activated partial thromboplastin times were associated with mortality in patients with SFTS. Two outbreaks of nosocomial SFTS transmission were observed. Conclusions SFTS is an endemic disease in South Korea, with a nationwide distribution and a high case-fatality ratio. Confusion, elevated levels of C-reactive protein, and prolonged activated partial thromboplastin times were associated with mortality in patients with SFTS. PMID:28033338
The genome of tomato (Solanum lycopersicum) is being sequenced by an international consortium of 10 countries (Korea, China, the United Kingdom, India, the Netherlands, France, Japan, Spain, Italy and the United States) as part of a larger initiative called the ‘International Solanaceae Genome Proje...
Korea in order to deter an attack by the Democratic Peoples ’ Republic of Korea. This paper examines the security alliance that exists between the...region: The Republic of Korea, the Democratic Peoples ’ Republic of Korea, the Peoples ’ Republic of China, Japan and the Russian Federation. This paper...of Korea (ROK), Alliance, South Korea, North Korea, Democratic Peoples ’ Republic of Korea (DPRK), United States Forces Korea (USFK), Korea Command
The InterLymph Consortium, or formally the International Consortium of Investigators Working on Non-Hodgkin's Lymphoma Epidemiologic Studies, is an open scientific forum for epidemiologic research in non-Hodgkin's lymphoma.
Helzer, John E.
Reviews the application of epidemiology to alcoholism. Discusses measurement and diagnostic issues and reviews studies of the prevalence of alcoholism, its risk factors, and the contributions of epidemiology to our knowledge of treatment and prevention. (Author/KS)
Apfelbacher, C J; Diepgen, T L; Weisshaar, E
Dermato-epidemiology is an important scientific discipline which investigates skin diseases using epidemiological methods. Epidemiology is the science of the distribution and determinants of disease in specified populations. We describe fundamental terms of dermato-epidemiology (measures of disease occurrence, measures of risk), different study types (observational studies, interventional studies), the selection of statistical tests, bias and confounding as well as the principles of evidence-based dermatology, and give illustrative examples.
Jeon, Hyeong-Kyu; Park, Hansol; Lee, Dongmin; Choe, Seongjun; Kim, Kyu-Heon; Huh, Sun; Sohn, Woon-Mok; Chai, Jong-Yil; Eom, Keeseon S
Tapeworms of the genus Spirometra are pseudophyllidean cestodes endemic in Korea. At present, it is unclear which Spirometra species are responsible for causing human infections, and little information is available on the epidemiological profiles of Spirometra species infecting humans in Korea. Between 1979 and 2009, a total of 50 spargana from human patients and 2 adult specimens obtained from experimentally infected carnivorous animals were analyzed according to genetic and taxonomic criteria and classified as Spirometra erinaceieuropaei or Spirometra decipiens depending on the morphology. Morphologically, S. erinaceieuropaei and S. decipiens are different in that the spirally coiled uterus in S. erinaceieuropaei has 5-7 complete coils, while in S. decipiens it has only 4.5 coils. In addition, there is a 9.3% (146/1,566) sequence different between S. erinaceieuropaei and S. decipiens in the cox1 gene. Partial cox1 sequences (390 bp) from 35 Korean isolates showed 99.4% (388/390) similarity with the reference sequence of S. erinaceieuropaei from Korea (G1724; GenBank KJ599680) and an additional 15 Korean isolates revealed 99.2% (387/390) similarity with the reference sequences of S. decipiens from Korea (G1657; GenBank KJ599679). Based on morphologic and molecular databases, the estimated population ratio of S. erinaceieuropaei to S. decipiens was 35: 15. Our results indicate that both S. erinaceieuropaei and S. decipiens found in Korea infect humans, with S. erinaceieuropaei being 2 times more prevalent than S. decipiens. This study is the first to report human sparganosis caused by S. decipiens in humans in Korea.
Jung, Bong-Kwang; Song, Hyemi; Kim, Min-Jae; Cho, Jaeeun; Shin, Eun-Hee; Chai, Jong-Yil
Toxoplasma gondii is an intracellular protozoan that can modulate the environment of the infected host. An unfavorable environment modulated by T. gondii in the brain includes tumor microenvironment. Literature has suggested that T. gondii infection is associated with development of brain tumors. However, in Korea, epidemiological data regarding this correlation have been scarce. In this study, in order to investigate the relationship between T. gondii infection and brain tumor development, we investigated the seroprevalence of T. gondii among 93 confirmed brain tumor patients (various histological types, including meningioma and astrocytoma) in Korea using ELISA. The results revealed that T. gondii seropositivity among brain tumor patients (18.3%) was significantly (P<0.05) higher compared with that of healthy controls (8.6%). The seropositivity of brain tumor patients showed a significant age-tendency, i.e., higher in younger age group, compared with age-matched healthy controls (P<0.05). In conclusion, this study supports the close relationship between T. gondii infection and incidence of brain tumors. PMID:27180580
Bae, Si Hyun; Yoon, Seung Kew; Jang, Jeong Won; Kim, Chang Wook; Nam, Soon Woo; Choi, Jong Young; Kim, Boo Sung; Park, Young Min; Suzuki, Seiji; Sugauchi, Fuminaka
Hepatitis B virus (HBV) is one of the major causative agents of chronic liver diseases in Korea. HBV has been classified into 8 genotypes by a divergence of >8% in the entire genomic sequence, and have distinct geographic distributions. There are limited data on the relevance between HBV genotypes and clinical outcomes in Korea. To investigate the clinical feature relating to HBV genotype in Korea, a total 120 serum samples with HBsAg (65 from Seoul and 55 from the other city in Korea) were obtained from each 30 chronic HBV carriers with asymptomatic carrier (ASC), chronic hepatitis (CH), liver cirrhosis (LC) and hepatocellular carcinoma (HCC). HBV genotype was determined by either enzyme-linked immunosorbent assay (ELISA) using monoclonal antibodies against genotype-specific epitopes in the preS2-region or the direct sequencing of small S gene. HBV genotypes were determined in 105 (87.5%) of 120 samples. HBV genotype C was identified in all HBV carriers with ASC, CH, LC, and HCC. Genotypes A, B, D, E, F and G were not detected in any of them. Genotype C HBV prevails predominantly among chronic carriers of the virus in Korea, irrespective of their clinical stages of liver disease and geographic origin. PMID:16224156
Lee, Yong-Jik; Lee, Sang-Jae; Jeong, Haeyoung; Kim, Hyun Ju; Ryu, Naeun; Kim, Byoung-Chan; Lee, Han-Seung; Lee, Dong-Woo; Lee, Sang Jun
Bacillus oceanisediminis 2691 is an aerobic, Gram-positive, spore-forming, and moderately halophilic bacterium that was isolated from marine sediment of the Yellow Sea coast of South Korea. Here, we report the draft genome sequence of B. oceanisediminis 2691 that may have an important role in the bioremediation of marine sediment.
For government officials in South Korea, it's a vision worth savoring: Within the next decade, South Korea becomes Southeast Asia's top higher-education destination, poaching thousands of Chinese, Indian, and Japanese students from American universities and overtaking rivals Singapore, Malaysia, and Hong Kong. The higher-education system's…
Amsden, Asia’s Next Giant: South Korea and Late Industralization (Oxford: Oxford University Press, 1989). 17 manage the absorption of North Korea by...is to use this new airport as a light industry and biotechnology hub with easy com- munications and transportation to and from China, Japan, Russia
Park, Hyunjoon; Raymo, James M.
The authors extend comparative research on educational differences in divorce by analyzing data from Korea. A primary motivation was to assess whether the theoretically unexpected negative educational gradient in divorce in Japan is also observed in Korea. Using vital statistics records for marriages and divorces registered between 1991 and 2006,…
U.S. intelligence discovered in the 1980s that North Korea was building a small nuclear reactor. The reactor was described as a gas-cooled, graphite-moderated model similar to those Britian and France used to produce electric power as well as plutonium for nuclear weapons. When Western nations expressed concern about the reactor Russia pressed North Korea to sign the Non-Proliferation Treaty (NPT) which it did on December 12, 1985. However, North Korea stalled on signing the required safeguards agreement that allows the International Atomic Energy Agency (IAEA) to inspect nuclear facilities until January 1992. Inspections by the IAEA revealed discrepancies with the amounts of plutonium separated as declared by the North Koreans. The IAEA also received reports that two North Korean waste sites were hidden. By February 1993 the IAEA and the North Koreans has reached an impasse: North Koreas initial declarations of plutonium inventory could not be confirmed and North Korea refused to cooperate. At the least, North Korea admits to having separated 100 grams of plutonium. At the most, worst case estimate, they could have a total of 6 - 13 kilograms of separated plutonium. A first nuclear weapon can require up to 10 kilograms of weapon-grade plutonium. Any settlement needs to include a way to insure that the IAEA can verify North Korea`s past nuclear activities and determine the amount of plutonium that may have been separated in the past. 2 refs.
This article reports that construction is nearing completion on Pyongyang University of Science and Technology in North Korea, in which academics from around the world will teach the best of the country's graduate students. This will be North Korea's first international university and will let the world know that the capacity of their scientists…
Moon, Hyun-Woo; Lee, Byung-Woo; Sung, Haan Woo; Yoon, Byung-Il; Kwon, Hyuk Moo
A new avian hepatitis E virus (HEV) GI-B was identified in broiler breeders with hematomas, liver rupture, and splenomegaly, along with excessive abdominal fat, in Korea. Previously, genotype 1 had been identified in avian HEV strains in Korea. Complete sequence analyses revealed that the new avian HEV clustered in genotype 2, which has been identified in the USA and Spain; the GI-B isolate was closely related to the USA prototype avian HEV isolated from a chicken with hepatitis-splenomegaly syndrome. Although some HEV genotypes show a geographical distribution pattern, the discovery of genotype 2 in addition to genotype 1 in Korea suggests that the geographical grouping might be reconsidered. These findings have important implications for understanding the global epidemiology and spread of avian HEV.
Yoo, Jeong Rae; Heo, Sang Taek; Park, Dahee; Kim, Hyemin; Fukuma, Aiko; Fukushi, Shuetsu; Shimojima, Masayuki; Lee, Keun Hwa
Severe fever with thrombocytopenia syndrome (SFTS) is tick-borne viral disease that was first suspected in China in 2009. The causative virus (SFTSV) was isolated in 2009 and reported in 2011, and SFTSV expanded its geographic distribution in 2012–2013, from China to South Korea and Japan. Most SFTSV infections occur through Haemaphysalis longicornis. However, SFTSV infection can also occur between family members, and nosocomial transmission of SFTSV is also possible through close contact with a patient. In this study, we first analyzed clinical, epidemiological, and laboratory data for SFTS patients and family members of an index patient in Korea. The S segment of SFTSV was amplified from the sera of three patients, and the S segment of SFTSV and IgG specific to SFTSV were detected in the serum from one family member; although this individual had no history of exposure to H. longicornis, she frequently had close contact with the index patient. In Korea, SFTSV infection among family members does not have to be reported, and we suggest that person-to-person transmission of SFTSV among family members is possible in Korea. PMID:27928083
ct/rls/crt/2006/82736.htm] at p. 147. 28 Yi Sang-il and Chin Se-ku. Yongbyon nuclear facility can be disabled within a year. JongAng Ilbo (internet...Interview of the President by Foreign Print Media, August 30, 3007. 32 Choe Sang- hun and David E. Sanger, North Korea claims U.S. will remove sanctions...smuggle conventional arms, including machine guns , automatic rifles, and anti-tank rocket launchers, to the Tamil Tigers in Sri Lanka. The Sri Lankan
Lim, Sooyeon; Lee, Dong-Hoon; Kwak, Woori; Shin, Hakdong; Ku, Hye-Jin; Lee, Jong-Eun; Lee, Gun Eui; Kim, Heebal; Choi, Sang-Ho; Ryu, Sangryeol; Lee, Ju-Hoon
Staphylococcus aureus is an important foodborne pathogen that causes diverse diseases ranging from minor infections to life-threatening conditions in humans and animals. To further understand its pathogenesis, the genome of the strain S. aureus FORC_001 was isolated from a contaminated food. Its genome consists of 2,886,017 bp double-stranded DNA with a GC content of 32.8%. It is predicted to contain 2,728 open reading frames, 57 tRNAs, and 6 rRNA operons, including 1 additional 5S rRNA gene. Comparative phylogenetic tree analysis of 40 complete S. aureus genome sequences using average nucleotide identity (ANI) revealed that strain FORC_001 belonged to Group I. The closest phylogenetic match was S. aureus MRSA252, according to a whole-genome ANI (99.87%), suggesting that they might share a common ancestor. Comparative genome analysis of FORC_001 and MRSA252 revealed two non-homologous regions: Regions I and II. The presence of various antibiotic resistance genes, including the SCCmec cluster in Region I of MRSA252, suggests that this strain might have acquired the SCCmec cluster to adapt to specific environments containing methicillin. Region II of both genomes contains prophage regions but their DNA sequence identity is very low, suggesting that the prophages might differ. This is the first report of the complete genome sequence of S. aureus isolated from a real foodborne outbreak in South Korea. This report would be helpful to extend our understanding about the genome, general characteristics, and virulence factors of S. aureus for further studies of pathogenesis, rapid detection, and epidemiological investigation in foodborne outbreak.
... 178 RIN 1515-AD86 United States-Korea Free Trade Agreement AGENCIES: U.S. Customs and Border... United States-Korea Free Trade Agreement entered into by the United States and the Republic of Korea.... SUPPLEMENTARY INFORMATION: Background On June 30, 2007, the United States and the Republic of Korea...
In this article, current status of noise exposure in workplaces, trend of workers with noise-induced hearing loss (NIHL), and prevalence of NIHL in workers by industry and job category in Korea were reviewed. In addition, trends of research on the audiological effects such as hearing loss from noise and occupational hearing loss from non-noise in Korea were addressed through reports in industrial audiology. Though noise exposure level has improved, noise still shows the highest rate of cases exceeding exposure limit among workplace hazards. NIHL is the most common occupational disease except work-related disease such as musculoskeletal disorders and cerebrovascular diseases, and NIHL prevalence is thought to be much higher than reported in official publications. Noise affecting hearing comes from various sources such as workplaces, military settings, areas with exposure to high noise, and specific noise sources. There is also occupational hearing loss by non-noise including chemicals such as organic solvents and heavy metals, barotrauma, and trauma due to welding spark. Noise affects daily life through audiological effects such as hearing loss and tinnitus, non-audiological physical effects (e.g., cardiovascular), and psychosocial and behavioral effects. Development of systematic and comprehensive hearing conservation programs for lowering the noise level in workplaces and preventing the NIHL, and preparation of technological, administrative system for its settlement at workplace are urgently needed. PMID:21258593
Jeong, Kyoung Yong
Arthropods are important in human health, which can transmit pathogens to humans, parasitize, or produce important allergens. Allergy prevalence becomes higher in Korea recently as well as other developed countries in contrast to a decrease of infectious diseases. Allergic diseases caused by household arthropods have increased dramatically during the last few decades since human beings spend more their time for indoor activities in modernized life style. Household arthropods are one of the most common causes of allergic diseases. Biological characterization of household arthropods and researches on their allergens will provide better understanding of the pathogenesis of allergic diseases and suggest new therapeutic ways. Therefore, studies on arthropods of allergenic importance can be considered one of the major research areas in medical arthropodology and parasitology. Here, the biology of several household arthropods, including house dust mites and cockroaches, the 2 most well known arthropods living indoor together with humans worldwide, and characteristics of their allergens, especially the research activities on these allergens performed in Korea, are summarized. PMID:19885330
Kim, Kyoo Sang
In this article, current status of noise exposure in workplaces, trend of workers with noise-induced hearing loss (NIHL), and prevalence of NIHL in workers by industry and job category in Korea were reviewed. In addition, trends of research on the audiological effects such as hearing loss from noise and occupational hearing loss from non-noise in Korea were addressed through reports in industrial audiology. Though noise exposure level has improved, noise still shows the highest rate of cases exceeding exposure limit among workplace hazards. NIHL is the most common occupational disease except work-related disease such as musculoskeletal disorders and cerebrovascular diseases, and NIHL prevalence is thought to be much higher than reported in official publications. Noise affecting hearing comes from various sources such as workplaces, military settings, areas with exposure to high noise, and specific noise sources. There is also occupational hearing loss by non-noise including chemicals such as organic solvents and heavy metals, barotrauma, and trauma due to welding spark. Noise affects daily life through audiological effects such as hearing loss and tinnitus, non-audiological physical effects (e.g., cardiovascular), and psychosocial and behavioral effects. Development of systematic and comprehensive hearing conservation programs for lowering the noise level in workplaces and preventing the NIHL, and preparation of technological, administrative system for its settlement at workplace are urgently needed.
Since 1970s, the economic and social development in South Korea, as well as dietary pattern, has undergone various changes. Concerns for the decreased nutrition quality and physical activities among Koreans, especially young population, call for a need of a holistic approach in national food and nutrition policy. The National Health Promotion Act of 1995 included national interventions and programs to deal with nutrition-related chronic diseases and obesity prevention. A nation-wide monitoring system, which includes nutrition and health examination survey, is being built and run by the Ministry of Health and Welfare and its affiliated organizations every three years. The Korea Food and Drug Administration (KFDA) is another key agency undertaking national food and nutrition policies. The KFDA recently promulgated the national strategic plans for improving food safety and nutrition, focusing on children. Nutrition labelling policy for processed food is managed by KFDA and various education programs are developed and disseminated to enhance the awareness of nutrition labelling. The agency also makes standards and regulates foods for special dietary uses and health functional food. The Rural Development Administration (RDA) is responsible for maintaining the food composition database. Finally, the National School Lunch Program is mainly governed by the Ministry of Education and Human Resources Development. The above central government agencies along with regional health centers are making efforts to promote the healthy eating habits in addition to constructing healthy environment by making laws and programs and by research and social marketing.
Su, Shuo; Wong, Gary; Shi, Weifeng; Liu, Jun; Lai, Alexander C K; Zhou, Jiyong; Liu, Wenjun; Bi, Yuhai; Gao, George F
Human coronaviruses (HCoVs) were first described in the 1960s for patients with the common cold. Since then, more HCoVs have been discovered, including those that cause severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS), two pathogens that, upon infection, can cause fatal respiratory disease in humans. It was recently discovered that dromedary camels in Saudi Arabia harbor three different HCoV species, including a dominant MERS HCoV lineage that was responsible for the outbreaks in the Middle East and South Korea during 2015. In this review we aim to compare and contrast the different HCoVs with regard to epidemiology and pathogenesis, in addition to the virus evolution and recombination events which have, on occasion, resulted in outbreaks amongst humans.
Kim, Yong Kwan; Lim, Seong-In; Kim, Jae-Jo; Cho, Yoon-Young; Song, Jae-Young; Cho, In-Soo; Hyun, Bang-Hun; Choi, Sung-Hyun; Kim, Seung-Hoe; Park, Eun-Hye; An, Dong-Jun
Classical swine fever (CSF) is a highly contagious systemic hemorrhagic viral disease of pigs. Wild boar plays a crucial role in the epidemiology of CSF. Between 2010 and 2014, samples were collected nationwide from 6,654 wild boars hunted in South Korea. Anti-CSF antibodies were identified in 0.59% (39 of 6,654) of the wild boar samples using a virus neutralization test and were primarily detected in wild boars living close to the demilitarized zone and the area of the Taebaek Mountains surroundings. The CSF virus (subgroup 2.1b) was isolated from two wild boars captured in a nearby border area. The criteria used to define high-risk areas for targeted CSF surveillance in South Korea should be further expanded to include other regions nationwide.
The concept of meta-epidemiology has been introduced with considering the methodological limitations of systematic review for intervention trials. The paradigm of meta-epidemiology has shifted from a statistical method into a new methodology to close gaps between evidence and practice. Main interest of meta-epidemiology is to control potential biases in previous quantitative systematic reviews and draw appropriate evidences for establishing evidence-base guidelines. Nowadays, the network meta-epidemiology was suggested in order to overcome some limitations of meta-epidemiology. To activate meta-epidemiologic studies, implementation of tools for risk of bias and reporting guidelines such as the Consolidated Standards for Reporting Trials (CONSORT) should be done.
Lee, Hyukmin; Unemo, Magnus; Kim, Hyo Jin; Seo, Younghee; Lee, Kyungwon; Chong, Yunsop
Objectives Antimicrobial resistance (AMR) in Neisseria gonorrhoeae is a major concern globally; however, no comprehensive AMR data for gonococcal isolates cultured after 2006 in Korea have been published internationally. We determined the susceptibility of N. gonorrhoeae isolates cultured in 2011–13, the mechanism of extended-spectrum cephalosporin (ESC) resistance and the molecular epidemiology of gonococcal strains in Korea. Methods In 2011–13, 210 gonococcal isolates were collected in Korea and their AMR profiles were examined by the agar dilution method. The penA, mtrR, penB, ponA and pilQ genes were sequenced in 25 isolates that were resistant to ESCs and 70 randomly selected isolates stratified by year. For molecular epidemiology, N. gonorrhoeae multiantigen sequence typing and MLST were performed. Results None of the N. gonorrhoeae isolates was susceptible to penicillin G and most were resistant to tetracycline (50%) and ciprofloxacin (97%). The rates of resistance to ceftriaxone, azithromycin, cefpodoxime and cefixime were 3%, 5%, 8% and 9%, respectively. However, all isolates were susceptible to spectinomycin. Twenty-one (84%) of the 25 ESC-resistant isolates contained the non-mosaic PBP2 XIII allele; however, the remaining 4 (16%) possessed the mosaic PBP2 X allele, which has been previously associated with ESC resistance including treatment failures. Conclusions In Korea, susceptibility to spectinomycin remains high. However, the recent emergence of ESC-resistant N. gonorrhoeae strains, including strains possessing the PBP2 mosaic X and non-mosaic XIII alleles, is a major concern and enhanced AMR surveillance is necessary to prevent transmission of these strains. PMID:26084303
Viale, M N; Zumárraga, M J; Araújo, F R; Zarraga, A M; Cataldi, A A; Romano, M I; Bigi, F
The species Mycobacterium bovis and Mycobacterium avium subspecies paratuberculosis are the causal agents, respectively, of tuberculosis and paratuberculosis in animals. Both mycobacteria, especially M. bovis, are also important to public health because they can infect humans. In recent years, this and the impact of tuberculosis and paratuberculosis on animal production have led to significant advances in knowledge about both pathogens and their host interactions. This article describes the contribution of genomics and functional genomics to studies of the evolution, virulence, epidemiology and diagnosis of both these pathogenic mycobacteria.
Chang, Hyuk Won; Suh, Sang-il; Jeong, Hae Woong; Suh, Dae Chul
Carotid artery angioplasty with stenting (CAS) is being performed in many hospitals in Korea. Most of the guidelines which are being used are similar, but the practical aspects such as techniques are different between hospitals. For example, usage of various protective devices, the oral antiplatelet regimen prior to procedure and placing of temporary pacemaker to prevent bradycardia are different between hospitals. In this article, we summarize and propose the guidelines for CAS which is currently being accepted in Korea. These guidelines may be helpful in providing protocol to neurointerventionalist who perform CAS and to standardize the process including reporting of CAS in the future comparative trials in Korea. PMID:25763292
The ABWR and SBWR design, both under development at GE, provide the best platform for developing the next generation advanced plants. The ABWR, which is rapidly setting the standard for new nuclear reactor plants, is clearly the best choice to meet the present energy needs of Korea. And through a GE/Korea partnership to develop the plant of the next century, Korea will establish itself as a leader in innovative reactor technology.
The epidemiological transition describes the changes in the health profile of populations where infectious diseases are substituted by chronic or non-communicable diseases. Even in industrialized countries, infectious diseases emerge as important public health problems and with a very important association with several type of neoplasm. Molecular epidemiology brings in new tools for the study of the epidemiological transition by discovering infectious agents as etiology of diseases, neither of both new. Much has been advanced in the understanding of the virulence and resistance mechanism of different strains, or improving the knowledge on transmission dynamics and dissemination pathways of infectious diseases. As to the non-communicable diseases, molecular epidemiology has enhanced the identification of endogenous risk factors link to alterations, molecular changes in genetic material, that will allow a more detail definition of risk and the identification of individual and groups at risk of several diseases. The potential impact of molecular epidemiology in other areas as environmental, lifestyles and nutritional areas are illustrated with several examples.
Yoon, KiChang; Kim, Jae-Hun; Kim, Young Yun; Kwon, Yongki; Wi, Gwan-sik
The Korean Space Weather Center (KSWC) of the National Radio Research Agency (RRA) is a government agency which is the official source of space weather information for Korean Government and the primary action agency of emergency measure to severe space weather condition. KSWC's main role is providing alerts, watches, and forecasts in order to minimize the space weather impacts on both of public and commercial sectors of satellites, aviation, communications, navigations, power grids, and etc. KSWC is also in charge of monitoring the space weather condition and conducting research and development for its main role of space weather operation in Korea. In this study, we will present KSWC's recent efforts on development of application-oriented space weather research products and services on user needs, and introduce new international collaborative projects, such as IPS-Driven Enlil model, DREAM model estimating electron in satellite orbit, global network of DSCOVR and STEREO satellites tracking, and ARMAS (Automated Radiation Measurement for Aviation Safety).
Yoon, K.; Hong, S.; Park, S.; Kim, Y. Y.; Wi, G.
The Korean Space Weather Center (KSWC) of the National Radio Research Agency (RRA) is a government agency which is the official source of space weather information for Korean Government and the primary action agency of emergency measure to severe space weather condition. KSWC's main role is providing alerts, watches, and forecasts in order to minimize the space weather impacts on both of public and commercial sectors of satellites, aviation, communications, navigations, power grids, and etc. KSWC is also in charge of monitoring the space weather condition and conducting research and development for its main role of space weather operation in Korea. In this study, we will present KSWC's recent efforts on development of application-oriented space weather research products and services on user needs, and introduce new international collaborative projects, such as IPS-Driven Enlil model, global network of DSCOVR and STEREO satellites tracking, and ARMAS (Automated Radiation Measurement for Aviation Safety).
Bak, Tae-Jong; Jeon, Chan-Hyeok; Kim, Jeong-Ho
Chub mackerel (Scomber japonicus) is a pelagic fish species widely distributing in the Indo-Pacific and a commercially important fish species in Korea. It is known to harbor anisakid nematodes larvae, and ingesting the raw or undercooked fish can accidentally cause human infection. In this study, we isolated the nematode larvae in 417 chub mackerel caught from 7 sampling locations around the Korean Peninsula in 2011 and 2012, and identified them by PCR-RFLP of the ITS (internal transcribed spacer) of ribosomal DNA and the direct sequencing of the mitochondrial DNA cox2 gene. The prevalence of infection was 55.4% (231/417) and the mean intensity was 7.0 (1628/231). Most of the nematodes (1523/1628; 93.6%) were found in the body cavity, while 5.5% (89/1628) were found in the gastrointestinal tract. Four different species were identified by PCR-RFLP and direct sequencing. Most of the nematodes (1535/1628; 94.3%) were identified as Anisakis pegreffii, and 2.8% (46/1628) were identified as Hysterothylacium sp. A hybrid genotype (Anisakis simplex sensu stricto×A. pegreffii) and A. simplex sensu stricto were 2.5% (41/1628) and 0.4% (6/1628) of the identified nematodes, respectively. The anisakid nematode assemblage of chub mackerel in Korea was similar to that of chub mackerel from the Tsushima Current stock in Japan, in that A. pegreffii was the dominant species. Since most of the anisakid nematodes were found in the body cavity and most of them were identified as A. pegreffii or Hysterothylacium sp. by PCR-RFLP and direct sequencing, chub mackerel may not greatly contribute to human anisakidosis in Korea. Alternately, A. pegreffii may be responsible for human anisakidosis in Korea, in addition to A. simplex sensu stricto. Further studies, such as the molecular diagnosis of human anisakidosis, are necessary for assessing the epidemiological role of chub mackerel in Korea.
Kim, Ho-Youn; Song, Yeong-Wook
Rheumatology was first recognized as a distinct clinical specialty in Korea just 35 years ago. Young professors who were trained in rheumatology in the USA and afterwards returned to Korea contributed substantially to advances in rheumatology clinical practice, educational programmes and research activities. They also established the Korean Rheumatism Association, later renamed the Korean College of Rheumatology. These young rheumatologists had a major role not only in raising the level of clinical and scientific activities, but also in promoting academic exchanges around the Asia-Pacific region, the USA and Europe. Subsequently, Korea's rapid economic growth and high education level enabled rheumatology to advance rapidly. Today, continued efforts are required to raise the standard of clinical and basic research, to optimize clinical practice with regard to new biologic agents, to exploit personalized and targeted therapies for the rheumatic diseases, and to meet the medical demands of Korea's ageing society.
Gallucci, Robert L.
In this paper, I summarize the events leading to the negotiation of the Agreed Framework with North Korea. I also highlight the threats that result from the current situation, and some of the technical issues relevant to understanding events.
led Trans- Pacific Partnership (TPP) free trade agreement negotiations. Strategic Cooperation and the U.S.-ROK Alliance Dealing with North Korea...78.49 yrs.; North Korea = 69.2 yrs.) Infant Mortality: 4.01 deaths/1,000 live births (U.S. = 6.00) Fertility Rate: 1.24 children born/woman...its “interest” in joining the twelve-nation Trans- Pacific Partnership (TPP) free trade agreement 3
profiles/ap_mp_05.cfm ; Internet; accessed 11 March 2003; and World Almanac Education Group, Inc., The World Almanac and Book of Facts 2003 (New York...New York: World Almanac Books, 2003), 108, 771, 799, 801, 843. 15 Han Woo-Keun, The History of Korea (Seoul, Korea: The Eul-Yoo Publishing Company...January 2003. 37 World Almanac Education Group, Inc., The World Almanac and Book of Facts 2003 (New York, New York: World Almanac Books, 2003), 218. 38
Regional Disease Vector Ecology Profile: The Koreas Published and Distributed by the Armed Forces Pest Management Board Information... Ecology Profile: The Koreas 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER 5e. TASK NUMBER 5f...presumed to be higher in the absence of sophisticated programs to suppress vectors or limit disease transmission. Disease Vector Ecology Profiles
Choi; Hahm; Rhee; Han
During the 1980s and 1990s, Korea has invested heavily in biotechnology research and development, with the aim of becoming a leading nation in this field. It is important to understand the historical progress of this development in order to appreciate the current state of biotechology in Korea. However, it is equally important to know what research is currently being planned and carried out, and by whom.
Barata, Rita Barradas
The present essay deals with the relation between epidemiology and public policies, highlighting the epidemiology position in the public health field, analyzing the impact of public policies over epidemiological profile and contributions from epidemiology to the lay down, implementation and evaluation of public health policies. In the first title, the essay debates the links between the epidemiology and public health field, the social determinants and political action framework proposed by the WHO's Commission on Social Determinants of Health, and different approaches of health policies. In the second title the essay analyses the reduction of child stunting in Brazil as an example of public policies that impact epidemiological profile. The third title presents three strategic topics for the application of public health policies: reduction of social inequalities in health, health promotion and regulation of products and services that have impact over health. The fourth title discusses the possibilities and difficulties to combine the epidemiological knowledge in the lay down, implementation and evaluation of public policies and, finally, material examples of such relation between epidemiology and public policies are presented.
Kim, Ji Hyung; Kang, Do-Hyung
Here, we report the draft genome of cyanobacterium Leptolyngbya sp. KIOST-1 isolated from a microalgal culture pond in South Korea. The genome consists of 13 contigs containing 6,320,172 bp, and a total of 5,327 coding sequences were predicted. This genomic information will allow further exploitation of its biotechnological potential for alimentary purposes.
Kim, Ji Hyung
Here, we report the draft genome of cyanobacterium Leptolyngbya sp. KIOST-1 isolated from a microalgal culture pond in South Korea. The genome consists of 13 contigs containing 6,320,172 bp, and a total of 5,327 coding sequences were predicted. This genomic information will allow further exploitation of its biotechnological potential for alimentary purposes. PMID:27635005
Escalera-Zamudio, Marina; Nelson, Martha I.; Cobián Güemes, Ana Georgina; López-Martínez, Irma; Cruz-Ortiz, Natividad; Iguala-Vidales, Miguel; García, Elvia Rodríguez; Barrera-Badillo, Gisela; Díaz-Quiñonez, Jose Alberto; López, Susana; Arias, Carlos F.; Isa, Pavel
In this work, nineteen influenza A/H3N2 viruses isolated in Mexico between 2003 and 2012 were studied. Our findings show that different human A/H3N2 viral lineages co-circulate within a same season and can also persist locally in between different influenza seasons, increasing the chance for genetic reassortment events. A novel minor cluster was also identified, named here as Korea, that circulated worldwide during 2003. Frequently, phylogenetic characterization did not correlate with the determined antigenic identity, supporting the need for the use of molecular evolutionary tools additionally to antigenic data for the surveillance and characterization of viral diversity during each flu season. This work represents the first long-term molecular epidemiology study of influenza A/H3N2 viruses in Mexico based on the complete genomic sequences and contributes to the monitoring of evolutionary trends of A/H3N2 influenza viruses within North and Central America. PMID:25075517
Yamaoka, Y; Osato, M S; Sepulveda, A R; Gutierrez, O; Figura, N; Kim, J G; Kodama, T; Kashima, K; Graham, D Y
The predominant H. pylori strain circulating among geographic locations differs with regard to the genomic structure. This study determined whether structural subtypes of the cagA 3' repeat region could be used to identify the population of origin of H. pylori isolates. We examined 600 cagA-positive H. pylori (Colombia, 100; USA, 100; France, 100; Canada, 20; Italy, 20; Korea, 100; Japan, 100; Hong Kong, 20; Taiwan, 20; Vietnam, 20). The cagA 3' region was amplified by PCR using primers specific to Japanese and Western 3' cagA gene sequences. PCR using Japanese cagA primers resulted in PCR products in 99-6 % of strains from East Asia but no non-Asian strains. Conversely, PCR using Western cagA primers resulted in amplicons in 100% of non-Asian strains, and only one from East Asia. cagA genotyping is useful for molecular epidemiological studies as strains can be completely separated by differences in the cagA 3' region.
Sheen, D.; Shin, J.; You, S.; Rhie, J.
Ambient seismic noise has been widely used for imaging crustal structure as an alternative passive source, even where traditional seismic imaging is not possible due to low seismicity. Long before the sensational applications of seismic noise, the origin of the noise has already been studied to understand its nature and characteristics for several decades. In this study, we investigate the origin of microseism observed in South Korea. Annual spectrograms in the microseismic frequency range up to 0.4 Hz show coherent peaks at about 0.2 Hz in the winter, which is at the frequency band of the double-frequency microseism. However, the primary microseism is only rarely observed in South Korea when the Pacific typhoon is close to the Southern Sea of Korea. Polarization analysis and noise cross correlation indicate that the energy of the double-frequency microseism comes dominantly from the east of the Korean Peninsula. Comparison of the results from the operational wave model of the Korea Meteorological Administration and seismic data shows a strong correlation of spectral amplitude of seismic data with the significant wave heights and periods of ocean waves, implying that the primary and the double-frequency microseism observed in South Korea are generated at the Southern Sea of Korea and at nearby shorelines of the east coast of Japan, respectively.
This review article outlines the key concepts in vaccine epidemiology, such as basic reproductive numbers, force of infection, vaccine efficacy and effectiveness, vaccine failure, herd immunity, herd effect, epidemiological shift, disease modeling, and describes the application of this knowledge both at program levels and in the practice by family physicians, epidemiologists, and pediatricians. A case has been made for increased knowledge and understanding of vaccine epidemiology among key stakeholders including policy makers, immunization program managers, public health experts, pediatricians, family physicians, and other experts/individuals involved in immunization service delivery. It has been argued that knowledge of vaccine epidemiology which is likely to benefit the society through contributions to the informed decision-making and improving vaccination coverage in the low and middle income countries (LMICs). The article ends with suggestions for the provision of systematic training and learning platforms in vaccine epidemiology to save millions of preventable deaths and improve health outcomes through life-course. PMID:27453836
Chow, Wong-Ho; Devesa, Susan S.
We analyzed renal cell cancer incidence patterns in the United States and reviewed recent epidemiologic evidence with regard to environmental and host genetic determinants of renal cell cancer risk. Renal cell cancer incidence rates continued to rise among all racial/ethnic groups in the United States, across all age groups, and for all tumor sizes, with the most rapid increases for localized stage disease and small tumors. Recent cohort studies confirmed the association of smoking, excess body weight, and hypertension with an elevated risk of renal cell cancer, and suggested that these factors can be modified to reduce the risk. There is increasing evidence for an inverse association between renal cell cancer risk and physical activity and moderate intake of alcohol. Occupational exposure to TCE has been positively associated with renal cell cancer risk in several recent studies, but its link with somatic mutations of the VHL gene has not been confirmed. Studies of genetic polymorphisms in relation to renal cell cancer risk have produced mixed results, but genome-wide association studies with larger sample size and a more comprehensive approach are underway. Few epidemiologic studies have evaluated risk factors by subtypes of renal cell cancer defined by somatic mutations and other tumor markers. PMID:18836333
... International Trade Administration Large Residential Washers From the Republic of Korea: Final Affirmative... the Republic of Korea (Korea). For information on the estimated subsidy rates, see the ``Suspension of... Washers From the Republic of Korea: Preliminary Affirmative Countervailing Duty Determination...
Breilh, J; Granda, E
The innovation of epidemiology plays a crucial role in the development of the health sciences. The authors emphasize the importance of epistemological analysis related to scientific and technical production. They focus on the theoretical and methodological contributions of the principal Latin American groups in the field of epidemiology, stating their main accomplishments, issues and potentials. When reviewing those conceptual and practical innovations, the authors analyse the effects of broader historical conditions on scientific work. To them, Latin American contemporary innovative epidemiological research and production have developed clearly differentiated principles, methods and technical projections which have led to a movement of critical or 'social' epidemiology. The functionalist approach of conventional epidemiology, characterized by an empiricist viewpoint, is being overcome by a more rigorous and analytical approach. This new epidemiological approach, in which the authors as members of CEAS (Health Research and Advisory Center) are working, has selectively incorporated some of the technical instruments of conventional epidemiology, subordinating them to a different theoretical and logical paradigm. The new framework of this group explains the need to consider the people's objective situation and necessities, when constructing scientific interpretations and planning technical action. In order to accomplish this goal, epidemiological reasoning has to reflect the unity of external epidemiological facts and associations, the so-called phenomenological aspect of health, with the underlying determinants and conditioning processes or internal relations, which are the essence of the health-disease production and distribution process. Epidemiological analysis is considered not only as a problem of empirical observation but as a process of theoretical construction, in which there is a dynamic fusion of deductive and inductive reasoning.(ABSTRACT TRUNCATED AT 250
... APR1400 Standard Plant Design submitted by Korea Hydro and Nuclear Power Co., Ltd. (KHNP) and Korea... application for standard design certification of the APR1400 Standard Plant Design. The APR1400 stands for... advanced design features to enhance plant safety, economical efficiency, and convenience of operation...
Park, Kwang Sook; Yang, Mi Hwa; Lee, Chang Kyu; Song, Ki-Joon
Human parainfluenza viruses (HPIV) are important causes of respiratory tract infections in young children. To characterize the molecular epidemiology of an HPIV outbreak occurring in Korea during 2006, genetic analysis of 269 cell culture isolates from HPIV-infected children, was conducted using nested reverse transcription-PCR (RT-PCR). HPIV-1 was detected in 70.3% of tested samples (189/269). The detection rate of HPIV-2 and HPIV-3 was 1.5% (4/269) and 9.3% (25/269), respectively. Mixed HPIV-1, -2 and -3 infections were detected in 19.0% (51/269): HPIV-1 and HPIV-2 in 15, HPIV-1 and HPIV-3 in 26, HPIV-2 and HPIV-3 in 6, and HPIV-1, -2 and -3 in 4. Of these positive samples for three different types HIPV-1, -2, and -3, two each representative strains were selected, the full length of hemagglutinin-neuraminidase (HN) gene for HPIV was amplified by RT-PCR, and sequenced. Multiple alignment analysis, based on reference sequence of HPIV-1, -2, and -3 strains available in GenBank, showed that the identity of nucleotide and deduced amino acid sequences was 92.4-97.6% and 92.7-97.9%, respectively, for HPIV-1, 88.5-99.8% and 88.6-100% for HPIV-2, and 96.3-99.5% and 95.0-99.3% for HPIV-3, respectively. Phylogenetic analysis showed that HPIV-1, -2, and -3 strains identified in this study were closely related among the strains in the same type with no significant genetic variability. These results show that HPIV of multiple imported sources was circulating in Korea.
Stollenwerk, Nico; Jansen, Vincent A. A.
For a long time criticality has been considered in epidemiological models. We review the body of theory developed over the last twenty five years for the simplest models. It is at first glance difficult to imagine that an epidemiological system operates at a very fine tuned critical state as opposed to any other parameter region. However, the advent of self-organized criticality has given hints in how to interpret large fluctuations observed in many natural systems including epidemiological systems. We show some scenarios where criticality has been observed (e.g., measles under vaccination) and where evolution towards a critical state can explain fluctuations (e.g., meningococcal disease.)
Lee, Hyejung; Song, Woogeun; Kwak, Hae-Ryun; Kim, Jae-Deok; Park, Jungan; Auh, Chung-Kyoon; Kim, Dae-Hyun; Lee, Kyeong-Yeoll; Lee, Sukchan; Choi, Hong-Soo
Tomato yellow leaf curl virus (TYLCV) is a member of the genus Begomovirus of the family Geminiviridae, members of which are characterized by closed circular single-stranded DNA genomes of 2.7-2.8 kb in length, and include viruses transmitted by the Bemisia tabaci whitefly. No reports of TYLCV in Korea are available prior to 2008, after which TYLCV spread rapidly to most regions of the southern Korean peninsula (Gyeongsang-Do, Jeolla-Do and Jeju-Do). Fifty full sequences of TYLCV were analyzed in this study, and the AC1, AV1, IR, and full sequences were analyzed via the muscle program and bayesian analysis. Phylogenetic analysis demonstrated that the Korea TYLCVs were divided into two subgroups. The TYLCV Korea 1 group (Masan) originated from TYLCV Japan (Miyazaki) and the TYLCV Korea 2 group (Jeju/Jeonju) from TYLCV Japan (Tosa/Haruno). A B. tabaci phylogenetic tree was constructed with 16S rRNA and mitochondria cytochrome oxidase I (MtCOI) sequences using the muscle program and MEGA 4.0 in the neighbor-joining algorithm. The sequence data of 16S rRNA revealed that Korea B. tabaci was closely aligned to B. tabaci isolated in Iran and Nigeria. The Q type of B. tabaci, which was originally identified as a viruliferous insect in 2008, was initially isolated in Korea as a non-viruliferous insect in 2005. Therefore, we suggest that two TYLCV Japan isolates were introduced to Korea via different routes, and then transmitted by native B. tabaci.
Choi, Won Suk
Herpes zoster and post-herpetic neuralgia deteriorate the quality of life because of severe pain and complications, and cause considerable social and economic burden of disease. In 2012, herpes zoster vaccine was released in Korea. The efficacy of herpes zoster vaccine is known to be 51.3-66.5% among the aged over 60 and 69.8-72.4% among adults between 50 and 59. It is also known that preventive efficacy is maintained for at least 5 years. Although there can be local reactions such as redness, pain and swelling at the site of injection and systemic reaction such as headache and eruption after herpes zoster vaccination, most of the adverse reactions are minor and disappear within days by themselves. As it is a live vaccine, persons with severe immune-suppression and pregnant women should not be vaccinated with the vaccine. Currently, Korean Society of Infectious Diseases recommended for the aged over 60 to be vaccinated with herpes zoster vaccine by subcutaneous route. In this article, clinical aspects and burden of disease of herpes zoster, efficacy and effects of herpes zoster vaccine, and herpes zoster vaccine recommendation by Korean Society of Infectious Diseases are discussed.
Diabetes is one of the foremost public health issues worldwide that can lead to complications in many organ systems, and has become a significant cause of morbidity and mortality in Korea. According to data from the National Health Insurance Service (NHIS), about 2.7 million Koreans (8.0%) aged 30 years or older had type 2 diabetes mellitus (T2DM) in 2013. The prevalence of T2DM increased with age and rose from 5.6% in 2006 to 8.0% in 2013. Using data based on The Health Screening Service of the NHIS, 25% of Korean adults were reported to have prediabetes in 2013. The prevalence of an impaired fasting glucose tended to increase over time from 21.5% in 2006 to 25.0% in 2013. Even though nationwide health screening has been regularly conducted as a public service, the proportion of undiagnosed cases of diabetes was still reported to be on the higher side in the latest study. Based on the results of these epidemic studies, further actions will be needed to effectively implement lifestyle changes on a social level and increase measures for the early detection of diabetes to stem the tide of the epidemic. PMID:27586447
Than, Van Thai; Jeong, Sunyoung; Kim, Wonyong
Rotavirus infections continue to be the leading cause of severe diarrhea in young Korean children. Rotavirus data acquired from uninterrupted surveillance studies between 1989 and 2009 in South Korea were analyzed to better understand the genetic diversity and evolution. The relationship between rotaviruses and the currently licensed rotavirus vaccine viruses was also examined. The most prevalent rotavirus strains, with genotype G1P, followed by G3P, G4P, and G2P, accounted for approximately 76.7% of the total identified strains, and more recently, rotavirus G9P has significance increased to be the fifth most common genotype. Phylogenetic analyses underscored the heterogeneity between viral populations within each genotype, with different lineages and sub-lineages. Although the currently licensed rotavirus vaccines are effective, safe, and economical, additional data from rotavirus monitoring is necessary to evaluate the efficacy of these vaccines for their sustained use in South Korea. The present study provides comprehensive and up-to-date information regarding the epidemiology, genetic diversity, and evolution of the circulating rotaviruses in South Korea.
Juranek, Dennis D.
Research into the epidemiology of lice indicates that infestation is uncommon in blacks, more common in females than males, significantly higher in low income groups, and transmission is by way of articles of clothing. (JD)
Research collaborations between the National Health and Environmental Effects Research Laboratory (NHEERL) and the National Exposure Research Laboratory (NERL) centered on the development and application of exposure analysis tools in environmental epidemiology include the El Paso...
Cohort studies are fundamental for epidemiological research by helping researchers better understand the etiology of cancer and provide insights into the key determinants of this disease and its outcomes.
Asbestos is a carcinogen that causes diseases such as mesothelioma and lung cancer in humans. There was a sharp increase in the use of asbestos in Korea in the 1970s as Korea's economy developed rapidly, and asbestos was only recently banned from use. Despite the ban of its use, previously applied asbestos still causes many problems. A series of asbestos-related events that recently occurred in Korea have caused the general public to become concerned about asbestos. Therefore, it is necessary to take proper action to deal with asbestos-related events, such as mass outbreaks of mesothelioma among residents who lived near asbestos textile factories or asbestos mines. Although there have been no rapid increases in asbestos-related illnesses in Korea to date, such illnesses are expected to increase greatly due to the amount of asbestos used and long latency period. Decreasing the asbestos exposure level to levels as low as possible is the most important step in preventing asbestos-related illnesses in the next few decades. However, there is a lack of specialized facilities for the analysis of asbestos and experts to diagnose and treat asbestos-related illnesses in Korea; therefore, national-level concern and support are required. PMID:19543418
Kim, Hyoung Ryoul
Asbestos is a carcinogen that causes diseases such as mesothelioma and lung cancer in humans. There was a sharp increase in the use of asbestos in Korea in the 1970s as Korea's economy developed rapidly, and asbestos was only recently banned from use. Despite the ban of its use, previously applied asbestos still causes many problems. A series of asbestos-related events that recently occurred in Korea have caused the general public to become concerned about asbestos. Therefore, it is necessary to take proper action to deal with asbestos-related events, such as mass outbreaks of mesothelioma among residents who lived near asbestos textile factories or asbestos mines. Although there have been no rapid increases in asbestos-related illnesses in Korea to date, such illnesses are expected to increase greatly due to the amount of asbestos used and long latency period. Decreasing the asbestos exposure level to levels as low as possible is the most important step in preventing asbestos-related illnesses in the next few decades. However, there is a lack of specialized facilities for the analysis of asbestos and experts to diagnose and treat asbestos-related illnesses in Korea; therefore, national-level concern and support are required.
foodgrains. South Korea followed a conciliation policy toward North Korea under the administrations of Kim Dae-jung and Roh Moo-hyun; but the...market. The regime has spent little of several billion dollars in foreign exchange earnings since 1998 to import food or medicines . The regime has...within North Korea. Key principles of this conciliation policy have been: the extension of South Korean economic and humanitarian aid to North Korea, the
South Korea’s economic growth, has fallen off, forcing South Korea into new mar- kets. In 1984, the construction industry received a...are in - cluded in the calculation. Since the 1970s, South Korea and the United States have begun a new stage of extensive economic contact, although...The Japanese Outlook 78 The Korean Peninsula’s Future 80 6. US INTERESTS AND OPTIONS IN SOUTH KOREA 83 Carter Administration Korean Policy 83
Choi, K. C.; Woo, J. H.; Kim, H. K.; Lee, Y. M.; Kim, Y.; Heyes, C.; Lee, J. B.; Song, C. K.; Han, J.
A comprehensive and combined analysis of air pollution and climate change could reveal important synergies of emission control measures, which could be of high policy relevance. IIASA's GAINS model (The Greenhouse gas - Air pollution Interactions and Synergies) has been developed as a tool to identify emission control strategies that achieve given targets on air quality and greenhouse gas emissions at least costs. The GAINS-Korea Model, which is being jointly developed by Konkuk University and IIASA, should play an important role in understanding the impact of air quality improvements across the regions in Korea. Source-Receptor relationships (S-R) is an useful methodology in air pollution studies to determine the areas of origin of chemical compounds at receptor point, and thus be able to target actions to reduce pollutions. The GAINS model can assess the impact of emission reductions of sources on air quality in receptor regions based on S-R matrix, derived from chemical transport model. In order to develop S-R matrix for GAINS-Korea, the CAMx model with PSAT/OSAT tools was applied in this study. The coarse domain covers East Asia, and a nesting domain as main research area was used for Korea peninsula. To evaluate of S-R relationships, a modeling domain is divided into sixteen regions over South Korea with three outside of S. Korea countries (China, N. Korea and Japan) for estimating transboundary contributions. The results of our analysis will be presented at the conference.
Lee, Myunglip; Roh, Seong Woon; Lee, Hae-Won; Yim, Kyung June; Kim, Kil-Nam; Bae, Jin-Woo; Choi, Kwang-Sik; Jeon, You-Jin; Jung, Won-Kyo; Kang, Heewan
Strain PB92T of Pedobacter agri, which belongs to the family Sphingobacteriaceae, was isolated from soil in the Republic of Korea. The draft genome of strain PB92T contains 5,141,552 bp, with a G+C content of 38.0%. This is the third genome sequencing project of the type strains among the Pedobacter species. PMID:22740666
Lee, Bo-Ra; Oh, Su-Bin; Byun, Hi-Ryong
The characteristics of the drought occurrence in North Korea over a period of 56 years (1952-2007) were analyzed by region, compared with those of South Korea, and graphed as a drought map for easy detection of the drought's history. To assess them, the Effective Drought Index (EDI), which was calculated from the daily precipitation data for 109 grids of the Korean Peninsula, was used. The daily precipitation data were extracted from the Asian Precipitation Highly Resolved Observational Data Integration towards Evaluation of Water Resources (APHRODITE). The characteristics of the drought occurrence in North Korea were summed up in the following five points. First, North Korea was divided into four drought sub-regions: the Northeastern region (G1), the Northern region (G2), the Central region (G3), and the Southern region (G4). Second, droughts occurred most frequently in G1 (28) and G4 (28 events) and least frequently in G3 (15 events). Third, in all sub-regions, short-term droughts lasting less than 100 days were the most frequent (53 % or higher) and the longest drought lasted 2,911 days (June 30, 1973 to June 20, 1981), which occurred in G3. Fourth, short-term droughts occurred mainly in spring, mid-term droughts (100-500 days) in spring and summer, and long-term droughts (over 500 days) in summer. Fifth, a dry period (monthly mean EDI <0) appeared in all sub-regions between 1973 and 1981 and between 1990 and 1993, and a strong negative precipitation anomaly appeared during each of these periods. When compared to the droughts in South Korea, those in North Korea were less frequent, but the mean duration was longer. Until 1979, droughts occurred almost at the same time in North Korea as South Korea, but beginning in 1980, the time differences between two regions became larger. Thus, the characteristics of the drought occurrence in North and South Korea differ.
... COMMISSION Large Power Transformers From Korea Determination On the basis of the record \\1\\ developed in the... the United States is materially injured, by reason of imports from Korea of large power transformers... power transformers from Korea were being sold at LTFV within the meaning of section 733(b) of the...
... COMMISSION Large Power Transformers From Korea Determination On the basis of the record \\1\\ developed in the... Korea of large power transformers, provided for in subheadings 8504.23.00 and 8504.90.95 of the... of large power transformers from Korea. Accordingly, effective July 14, 2011, the...
... 15 Commerce and Foreign Trade 2 2012-01-01 2012-01-01 false Anti-terrorism: North Korea. 742.19...-CCL BASED CONTROLS § 742.19 Anti-terrorism: North Korea. (a) License Requirements. (1) All items on... anti-terrorism reasons require a license for export or reexport to North Korea. This includes all...
... 15 Commerce and Foreign Trade 2 2013-01-01 2013-01-01 false Anti-terrorism: North Korea. 742.19...-CCL BASED CONTROLS § 742.19 Anti-terrorism: North Korea. (a) License Requirements. (1) All items on... anti-terrorism reasons require a license for export or reexport to North Korea. This includes all...
... 15 Commerce and Foreign Trade 2 2011-01-01 2011-01-01 false Anti-terrorism: North Korea. 742.19...-CCL BASED CONTROLS § 742.19 Anti-terrorism: North Korea. (a) License Requirements. (1) All items on... anti-terrorism reasons require a license for export or reexport to North Korea. This includes all...
This article explores what immersion English education means in South Korea (henceforth Korea) and examines various related educational practices. The proposal for English immersion from the Presidential Transition Committee of the Lee administration in early 2008 has highlighted immersion education in Korea. Ironically, since the committee's…
Population aging in Korea is projected to be the most rapid among Organisation for Economic Co-operation and Development (OECD) countries between 2000 and 2050. However, social spending in Korea remains low, reflecting Korea's relatively young population, limited health and long-term care insurance coverage, and immaturity of its pension system.…
Seong, Somi; Popper, Steven W.; Goldman, Charles A.; Evans, David K.
In the late 1990s, the Korea Ministry of Education and Human Resources, in response to concern over the relatively low standing of the nation's universities and researchers, launched the Brain Korea 21 program BK21). BK21 seeks to make Korean research universities globally competitive and to produce more high-quality researchers in Korea. It…
... COMMISSION Large Residential Washers From Korea and Mexico Scheduling of the final phase of countervailing... the United States is materially retarded, by reason of subsidized imports from Korea and less-than-fair-value imports from Korea and Mexico of large residential washers, provided for in subheading...
... COMMISSION Large Residential Washers From Korea and Mexico Determinations On the basis of the record \\1... materially injured by reason of imports from Korea of large residential washers that are alleged to be sold in the United States at less than fair value (LTFV) and subsidized by the Government of Korea....
... COMMISSION Large Residential Washers From Korea and Mexico Determinations On the basis of the record \\1...)) (the Act), that an industry in the United States is materially injured by reason of imports from Korea... subsidized by the Government of Korea and sold in the United States at less than fair value (LTFV)....
... 15 Commerce and Foreign Trade 2 2010-01-01 2010-01-01 false Anti-terrorism: North Korea. 742.19...-CCL BASED CONTROLS § 742.19 Anti-terrorism: North Korea. (a) License Requirements. (1) All items on... anti-terrorism reasons require a license for export or reexport to North Korea. This includes all...
Choi, Y.; Kim, M.; Byun, Y.; Yi, H.; Chang, S.; Choi, J.; Sohn, J.; Moon, H.; Park, J.
In the evening of March 9, 2014, a fireball falling from north to south was observed in South Korea. Multiple explosions were heard and multiple videos recorded in cars from various places, suggesting that the fireball was separated into several pieces. Immediately thereafter, a series of discovery reports about meteorites from the southern part of South Korea followed and, as of today, three meteorites were confirmed and one meteorite, with a mass of about 20 kg, is pending. This discovery of a meteorite in South Korea occurs for the first time in 70 years. The overall trajectory of the fireball matches the area where meteorites were discovered. According to the preliminary analyses, the meteorite is an ordinary chondrite. The origin of the meteorite and its surface properties will be studied.
Choi, Byung Ho; Kim, Kyeong Ok; Choi, Jae Cheon
The highest tides in South Korea are found along the northwest coast between latitudes 36-38 degrees and the number of possible sites for tidal range power barrages to create tidal basins is great due to irregular coastlines with numerous bays. At present Lake Sihwa tidal power plant is completed. The plant is consisted of 10 bulb type turbines with 8 sluice gates. The installed capacity of turbines and generators is 254MW and annual energy output expected is about 552.7 GWh taking flood flow generation scheme. Three other TPP projects are being progressed at Garolim Bay (20 turbines with 25.4MW capacity), Kangwha (28 turbines with 25.4MW capacity), Incheon (44 or 48 turbines with 30 MW capacity) and project features will be outlined here. The introduction of tidal barrages into four major TPP projects along the Kyeonggi bay will render wide range of potential impacts. Preliminary attempts were performed to quantify these impacts using 2 D hydrodynamic model demonstrating the changes in tidal amplitude and phase under mean tidal condition, associated changes in residual circulation (indicator for SPM and pollutant dispersion), bottom stress (indicator for bedload movement), and tidal front (positional indicator for bio-productivity) in both shelf scale and local context. Tidal regime modeling system for ocean tides in the seas bordering the Korean Peninsula is designed to cover an area that is broad in scope and size, yet provide a high degree of resolution in strong tidal current region including off southwestern tip of the Peninsula (Uldolmok , Jangjuk, Wando-Hoenggan), Daebang Sudo (Channel) and Kyeonggi Bay. With this simulation system, real tidal time simulation of extended springneap cycles was performed to estimate spatial distribution of tidal current power potentials in terms of power density, energy density and then extrapolated annual energy density.
Virlogeux, Victor; Fang, Vicky J.; Park, Minah; Wu, Joseph T.; Cowling, Benjamin J.
The incubation period is an important epidemiologic distribution, it is often incorporated in case definitions, used to determine appropriate quarantine periods, and is an input to mathematical modeling studies. Middle East Respiratory Syndrome coronavirus (MERS) is an emerging infectious disease in the Arabian Peninsula. There was a large outbreak of MERS in South Korea in 2015. We examined the incubation period distribution of MERS coronavirus infection for cases in South Korea and in Saudi Arabia. Using parametric and nonparametric methods, we estimated a mean incubation period of 6.9 days (95% credibility interval: 6.3–7.5) for cases in South Korea and 5.0 days (95% credibility interval: 4.0–6.6) among cases in Saudi Arabia. In a log-linear regression model, the mean incubation period was 1.42 times longer (95% credibility interval: 1.18–1.71) among cases in South Korea compared to Saudi Arabia. The variation that we identified in the incubation period distribution between locations could be associated with differences in ascertainment or reporting of exposure dates and illness onset dates, differences in the source or mode of infection, or environmental differences. PMID:27775012
Moon, Jeong Mi; Chun, Byeong Jo; Cho, Yong Soo
The aim of this study was to examine epidemiologic data regarding acute herbicide or insecticide poisoning in adults from 2011 to 2014 at the national level in South Korea. Further, the association between governmental regulations involving pesticides and changes in pesticide poisoning occurrences over time was determined. Data were obtained from the emergency department (ED)-based Injury In-depth Surveillance system conducted by the Korea Center for Disease Control and Prevention (KCDC). Governmental regulations on pesticides were downloaded from the homepage of the Korea Rural Development Administration. Pesticides were classified according to guidelines provided by the World Health Organization (WHO) and by the respective Resistance Action Committee (RAC). Trends in the number of ED presentations and case fatality rate (CFR) due to pesticide poisoning were investigated. The overall CFR due to poisoning from herbicides or insecticides in adults in South Korea was 16.8% during 2011-2014. However, CFR significantly decreased over the 4-year period. The ED presentations of paraquat (PQ) poisoning fell significantly, whereas poisoning due to glyphosate, glufosinate, or combined herbicides increased markedly over the 4 years. Between 2011 and 2013, PQ was the most common pesticide poisoning, whereas glyphosate became the most frequent in 2014. PQ produced the highest rate of fatality followed by endosulfan. Although the frequency of PQ poisoning decreased, which may be attributed to governmental regulations, the CFR and incidence of pesticide poisoning in adults remain a public health concern that needs to be addressed.
Nunes, Alexandra; Gomes, João P
The Chlamydiaceae are a family of obligate intracellular bacteria characterized by a unique biphasic developmental cycle. It encompasses the single genus Chlamydia, which involves nine species that affect a wide range of vertebral hosts, causing infections with serious impact on human health (mainly due to Chlamydia trachomatis infections) and on farming and veterinary industries. It is believed that Chlamydiales originated ∼700mya, whereas C. trachomatis likely split from the other Chlamydiaceae during the last 6mya. This corresponds to the emergence of modern human lineages, with the first descriptions of chlamydial infections as ancient as four millennia. Chlamydiaceae have undergone a massive genome reduction, on behalf of the deletional bias "use it or lose it", stabilizing at 1-1.2Mb and keeping a striking genome synteny. Their phylogeny reveals species segregation according to biological properties, with huge differences in terms of host range, tissue tropism, and disease outcomes. Genome differences rely on the occurrence of mutations in the >700 orthologous genes, as well as on events of recombination, gene loss, inversion, and paralogous expansion, affecting both a hypervariable region named the plasticity zone, and genes essentially encoding polymorphic and transmembrane head membrane proteins, type III secretion effectors and some metabolic pathways. Procedures for molecular typing are still not consensual but have allowed the knowledge of molecular epidemiology patterns for some species as well as the identification of outbreaks and emergence of successful clones for C. trachomatis. This manuscript intends to provide a comprehensive review on the evolution, phylogeny, and molecular epidemiology of Chlamydia.
Park, Hyeon Jin; Park, Eun-Hye; Jung, Kyu-Won; Kong, Hyun-Joo; Won, Young-Joo; Lee, Joo Young; Yoon, Jong Hyung; Park, Byung-Kiu; Lee, Hyewon; Eom, Hyeon-Seok
Background The nationwide statistical analysis of hematologic malignancies in Korea has not been reported yet. Methods The Korea Central Cancer Registry and the Korean Society of Hematology jointly investigated domestic incidence rates and prevalence of hematologic malignancies occurred between 1999 and 2008, and analyzed survival rates of patients who were diagnosed between 1993 and 2008. Data of hematologic malignancies from 1993 to 2008 were obtained from the Korean National Cancer Incidence Data base. The crude incidence rates, age-specific incidence rates, age-standardized incidence rates, annual percentage change of incidence, and prevalence from 1999-2008 were calculated. Survival rates for patients diagnosed in 1993-2008 were estimated. Results In 2008, a total of 8,006 cases of hematologic malignancies were occurred, which comprised 4.5% of all malignancies. In all genders, non-Hodgkin lymphoma, myeloid leukemia, and multiple myeloma were most frequent diseases. In terms of age, ages between 60 and 69 were most prevalent. From 1999 to 2008, the age-standardized incidence rates increased from 10.2 to 13.7, and the annual percentage change was 3.9%. The 5-year survival rate increased from 38.2% during 1993-1995 to 55.2% during 2004-2008. As of January 2009, number of patients with 10-year prevalence was 33,130, and with 5- to 10-year prevalence was 10,515. Conclusion This is the first nationwide statistical report of hematologic malignancies in Korea. It could be used as the basic information to help investigate epidemiologic characteristics, evaluate progress during the past years, and establish future strategies for hematologic malignancies. Periodic statistical analysis of hematologic malignancies in Korea should be continued. PMID:22479275
Park, Kyung-Sik; Park, Moo-In; Shin, Jeong-Eun; Jung, Kee-Wook; Kim, Seong-Eun; Lee, Tae-Hee; Koo, Hoon-Sup
Constipation is a digestive symptom that is frequently seen in clinical practice. Its prevalence has been reported to be 2% to 20%, depending on geographical region. Despite the rapid development of medical science, systematic studies on constipation have been rarely conducted in Korea. Recently, guidelines on the diagnosis and treatment of functional gastrointestinal disorders, including constipation, were proposed by The Korean Society of Neurogastroenterology and Motility. These guidelines are expected to reflect the current situation regarding treatment of constipation in Korea. In this paper, practical constipation treatment methods that are in current use will be reviewed with reference to these recent guidelines. PMID:23019388
humanitarian aid. Sources: Kim Myong Chol, “Kim Jong-il shifts to plan B,” Asia Tiimes, May 21, 2009, Online edition. “North Korea begins ‘Plan C...Asia Times, October 14, 2009, Online edition. Zhang Lianqui, “There is a Dangerous Component in the ‘Warm Winter’ of the DPRK Nuclear Issue, Huanqiu...Boycott Six-Party Talks ,” The Wall Street Journal, April 14, 2009, Online version. 7 Denis D. Gray, “North Korea turns to air smuggling,” Associated
Lee, Jong-Kyung; Kwak, No-Seong; Kim, Hyun Jung
This study systemically analyzed data on the prevalence of foodborne pathogens and foodborne disease outbreaks to identify the priorities of foodborne infection risk management in Korea. Multiple correspondence analysis was applied to three variables: origin of food source, phase of food supply chain, and 12 pathogens using 358 cases from 76 original papers and official reports published in 1998-2012. In addition, correspondence analysis of two variables--place and pathogen--was conducted based on epidemiological data of 2357 foodborne outbreaks in 2002-2011 provided by the Korean Ministry of Food and Drug Safety. The results of this study revealed three distinct areas of food monitoring: (1) livestock-derived raw food contaminated with Campylobacter spp., pathogenic Escherichia coli, Salmonella spp., and Listeria monocytogenes; (2) multi-ingredient and ready-to-eat food related to Staphylococcus aureus; and (3) water associated with norovirus. Our findings emphasize the need to track the sources and contamination pathways of foodborne pathogens for more effective risk management.
Cho, Kyung Ja; Khang, Shin Kwang; Lee, Seung Sook; Koh, Jae Soo; Chung, Jin Haeng; Lee, Yong Sik; Shim, Yoon Sang
Cancers of the upper aerodigestive tract (UADT) constitute 3.5-4% of all malignancies. Since the majority of cases are squamous cell carcinomas which are related with epidemiologic factors, a different pattern of UADT cancer might be present between the Western and Asian populations. We performed a pathology based statistical study on UADT cancers in Korean patients. Cases from Korea Cancer Center Hospital, from January 1, 1988 through December 31, 1998, were subjected to the study. Among 2,842 cases, epithelial malignancies accounted for 87.8%, with squamous cell carcinoma as the major type (76.5%). The larynx was the most commonly affected site (26%), followed by the oral cavity (25.1%), oropharynx (13%), nasopharynx (9%), hypopharynx (8.4%), paranasal sinuses (6.4%), nasal cavity (6%) and salivary glands (6.1%). The percentage of squamous cell carcinoma was highest (98.7%) at the hypopharynx, and lowest at the nasal cavity (42.3%), which showed the most diverse tumor entities. Korean patients with UADT cancers presented with a higher incidence of non-epidermoid malignancy including sarcoma (1.5%) and malignant melanoma (1.4%), and a higher frequency of involvement of the sinonasal tract, compared with the Western patients. PMID:11850583
Lee, Ju Young; Shin, Kyoung Min; Cho, Sun-Mi
Objective The aim of this study was to examine the prevalence of Internet addiction in middle school students and to identify associated psychosocial risk factors and depression. Methods This study was part of a larger epidemiological study on childhood psychiatric disorders conducted in Osan, a city of Republic of Korea. We used IAS for internet addiction, K-YSR for subjects' emotional and behavioral problems and K-CDI for depressive symptoms. We used the data of n=1217 completed cases. We put on independent variables, which are sex, age, smoking and alcohol experiences, economic status, age of first Internet use, K-YSR and K-CDI score. Results The subjects consisted of addicted users (2.38%), over users (36.89%) and normal Internet users (60.72%). Attention problems, sex, delinquent problems, K-CDI scores, thought problems, age and aggressive behavior were predictable variables of internet addiction. Age of initial Internet use negatively predicted Internet addiction. Conclusion This result showed similar to other researches about sociodemographic, emotional or behavioral factors related to internet addiction. Generally, subjects with more severe internet addiction had more emotional or behavioral problems. It means that they already have had various difficulties when we found internet addiction of adolescents. Therefore it is necessary to evaluate whether the subjects have any emotional or behavioral troubles and to intervene to prevent internet addiction. PMID:25395968
Antibody titers to vaccine-preventable diseases such as tetanus, polio, measles, mumps, and rubella decline within 1-10 years after allogeneic or autologous hematopoietic stem cell transplantation (SCT) if the recipient is not vaccinated. Vaccine-preventable diseases such as pneumococcal diseases, Haemophilus influenzae type b infections, influenza, measles, and varicella can pose an increased risk for SCT recipients. Therefore, after SCT, the recipients should be routinely revaccinated. Vaccination recommendations have previously been developed and published by the European Group of Blood and Marrow Transplantation and the Centers for Disease Control, by the Infectious Diseases Society of America, and by the American Society for Blood and Marrow Transplantation in 2009. Different epidemiologies and strategies have existed in Korea. In 2012, the Korean Society of Infectious Diseases published "Vaccination for Adult" describing the guidelines for vaccination, one of the chapters assigned for vaccination of SCT recipients. The present article reviews the current available vaccination strategies for SCT recipients, their family members, and healthcare workers, with the focus on recent Korean perspectives. PMID:24396628
This change has accelerated the growth of both of their already booming economies . Beyond that, it has helped propel Beijing into a pivotal role of...South Korea and China normalized relations in 1992. This change has accelerated the growth of both of their already booming economies . Beyond that...and South Korea will provide an opportunity for Pyongyang to improve its economy , thereby strengthening its standing and legitimacy internationally
Morton, Newton E
Genetic epidemiology developed in the middle of the last century, focused on inherited causes of disease but with methods and results applicable to other traits and even forensics. Early success with linkage led to the localization of genes contributing to disease, and ultimately to the Human Genome Project. The discovery of millions of DNA markers has encouraged more efficient positional cloning by linkage disequilibrium (LD), using LD maps and haplotypes in ways that are rapidly evolving. This has led to large international programmes, some promising and others alarming, with laws about DNA patenting and ethical guidelines for responsible research still struggling to be born. PMID:14561327
Getoor, Lise; Rhee, Jeanne T; Koller, Daphne; Small, Peter
Molecular epidemiological studies can provide novel insights into the transmission of infectious diseases such as tuberculosis. Typically, risk factors for transmission are identified using traditional hypothesis-driven statistical methods such as logistic regression. However, limitations become apparent in these approaches as the scope of these studies expand to include additional epidemiological and bacterial genomic data. Here we examine the use of Bayesian models to analyze tuberculosis epidemiology. We begin by exploring the use of Bayesian networks (BNs) to identify the distribution of tuberculosis patient attributes (including demographic and clinical attributes). Using existing algorithms for constructing BNs from observational data, we learned a BN from data about tuberculosis patients collected in San Francisco from 1991 to 1999. We verified that the resulting probabilistic models did in fact capture known statistical relationships. Next, we examine the use of newly introduced methods for representing and automatically constructing probabilistic models in structured domains. We use statistical relational models (SRMs) to model distributions over relational domains. SRMs are ideally suited to richly structured epidemiological data. We use a data-driven method to construct a statistical relational model directly from data stored in a relational database. The resulting model reveals the relationships between variables in the data and describes their distribution. We applied this procedure to the data on tuberculosis patients in San Francisco from 1991 to 1999, their Mycobacterium tuberculosis strains, and data on contact investigations. The resulting statistical relational model corroborated previously reported findings and revealed several novel associations. These models illustrate the potential for this approach to reveal relationships within richly structured data that may not be apparent using conventional statistical approaches. We show that Bayesian
Cross-Sectional and Longitudinal Associations between Egg Consumption and Metabolic Syndrome in Adults ≥ 40 Years Old: The Yangpyeong Cohort of the Korean Genome and Epidemiology Study (KoGES_Yangpyeong)
Woo, Hye Won; Choi, Bo Youl; Kim, Mi Kyung
Since the 1970s, the public has been advised to limit egg consumption even though there is little evidence of any harmful effect of eggs on blood cholesterol. The purpose of this cross-sectional and prospective study was to evaluate the potential association between egg consumption and metabolic syndrome (MetS) and MetS components in adults ≥ 40 years in KoGES_Yangpyeong. Yangpyeong is a rural area in South Korea. A total of 2,887 subjects (men 1,115, women 1,772) were recruited from 2005 to 2009, based on a physical examination and questionnaires administered using standardized protocol. After excluding subjects who had MetS at baseline, 1,663 subjects (675 men, 958 women) were followed for 3.20 years (range: 0.34–8.70). During the follow-up period, MetS occurred in 289 subjects. More than 3 eggs per week was significantly associated with decreased risk of MetS in both men (RR = 0.46, 95% CI, 0.26–0.82, P for trend = 0.1093) and women (RR = 0.54, 95% CI, 0.31–0.93, P for trend 0.0325) compared to non-users. There was a cross-sectional inverse relationship between egg consumption and abdominal obesity in men and women. Also, prospectively, higher egg consumption in men was associated with a decreased risk of high fasting blood glucose (RR = 0.39, 95% CI, 0.22–0.67, P for trend = 0.0042) and high triglycerides (RR = 0.42, 95% CI, 0.22–0.80, P for trend = 0.1080). In conclusion, our findings suggest that higher egg consumption may reduce the risk of MetS both in men and women, and the risk of high fasting blood glucose and high triglycerides in men. Current guidelines regarding egg consumption may need to be re-visited for healthy middle-aged and elderly people. PMID:26808174
Suárez, Erick; Sariol, Carlos A; Burguete, Ana; Mclachlan, Geoffrey
A new door has been opened to health professionals since the completion of the map of the human genome was announced in 2003, coinciding with the 50th anniversary of the discovery of the DNA helical structure by Watson and Crick in 1953. The continuous updating of the technology has enabled scientists to simultaneously analyze thousands of variables for genome analysis. These advances have created new opportunities to locate genes, to assess the gene-gene relationship, to measure the gene-environment interaction, to describe gene products, and to evaluate the gene-disease relationship. In epidemiology, new strategies have been developed to determine cause-effect relationship in case-control studies and cohort studies. With the information provided by the Human Genome Project, new epidemiological designs and new statistical methodology have been developed. The addition of molecular biology to traditional epidemiological approaches has given birth to a new discipline known as genetic epidemiology. The objective of this paper is to provide an introduction to concepts needed for assessing the association between genes and specific diseases in population based studies. Firstly, a description of the genetic concepts is presented as a framework for the epidemiological designs and the statistical procedures that have been utilized in genetic epidemiology. Then, a description of the different designs in genetic epidemiology is presented with the most recent publications. Finally, some considerations in the statistical analysis for genetic epidemiology are discussed.
The recommendation of Popper's philosophy of science should be adopted by epidemiologists is disputed. Reference is made to other authors who have shown that the most constructive elements in Popper's ideas have been advocated by earlier philosophers and have been used in epidemiology without abandoning inductive reasoning. It is argued that Popper's denigration of inductive methods is particularly harmful to epidemiology. Inductive reasoning and statistical inference play a key role in the science; it is suggested that unfamiliarity with these ideas contributes to widespread misunderstanding of the function of epidemiology. Attention is drawn to a common fallacy involving correlations between three random variables. The prevalence of the fallacy may be related to confusion between deductive and inductive logic.
Winters, Brian R; Walsh, Thomas J
The purpose of this review is to integrate understanding of epidemiology and infertility. A primer on epidemiologic science and an example disease for which the design of epidemiologic investigations is readily apparent are provided. Key features of infertility that limit epidemiologic investigation are described and a survey of available data on the epidemiology of infertility provided. Finally, the work that must be completed to move this area of research forward is proposed, and, with this new perspective of "infertility as a disease," improvements envisioned in public health that may be gained through improved understanding of the epidemiology of male infertility.
CGEMS identifies common inherited genetic variations associated with a number of cancers, including breast and prostate. Data from these genome-wide association studies (GWAS) are available through the Division of Cancer Epidemiology & Genetics website.
Australian Dept. of Labour and National Service, Perth.
THE POPULATION OF THE REPUBLIC OF KOREA WAS 27,184,000 IN 1963. AGRICULTURAL AND INDUSTRIAL PRODUCTION, ADVERSELY AFFECTED BY THE KOREAN WAR, HAS RECEIVED EMPHASIS THROUGH EXPORT PROMOTION, TAX REFORM, AND A STABILIZATION PROGRAM. A 6-YEAR FREE COMPULSORY EDUCATION IS SUPPLEMENTED BY "CIVIC SCHOOLS" AND "HIGHER CIVIC SCHOOLS"…
Lee, Hee-Il; Che, Il-Young; Kim, Tae Sung
Over the ten years after the installation of our first seismo-acoustic array station (CHNAR) in September 1999, Korea Institute of Geoscience and Mineral Resources (KIGAM) has been continuously observing infrasound with an infrasound array network, named KIN (Korean Infrasound Network) in Korea. This network consists of seven seismo-acoustic arrays (BRDAR, KMPAR, CHNAR, YAGAR, KSGAR, ULDAR and TJIAR). The aperture size of the smallest array (KMPAR and TJIAR) is about 300m and the largest is about 1.4km. The number of acoustic gauges are between 4 (TJIAR) and 18 (YAGAR), and 1 or 5 seismometers are collocated at the center of the acoustic array. All seismic and infrasonic signals of the arrays are digitized at 40 samples/sec and transmitted to KIGAM in real time. Many interesting infrasound signals associated with different kind of anthropogenic source as well as natural one are detected by KIN. Ten years of seismo-acoustic data are analyzed by using PMCC program, and identified more than five thousand of infrasonic events and catalogued in our infrasound database. This database is used to study characteristics of seasonally dependent propagation of the infrasound wave in local scale, as well as to better understand how atmospheric condition affects the detection ratio at a specific station throughout the year. It also played a valuable role in discriminating the anthropogenic events such as the second nuclear test on 25 May 2009 in North Korea, from natural earthquakes, which is important in estimating the seismicity in Korea.
5e. TASK NUMBER 5f. WORK UNIT NUMBER 7. PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES) School of Advanced Military Studies 250 Gibbon Ave. Ft...Soviet Union’s 53 Finley, The US Military Experience 1871-1982, 42. 54 Ibid., 43-44. 55 Ibid., 6. 56 Alan R. Millett, The War for Korea, 1950-1951
The Republic of Korea has transformed itself over the last 50 years from a nation based primarily on agriculture to a hi-tech industrial powerhouse. But now the country is seeing the importance of investing in fundamental science too, as Matin Durrani reports.
All facilities of the Ministry of Communications of Korea, which monopolizes telecommunications services in the country, are listed and described. Both domestic facilities, including long-distance telephone and telegraph circuits, and international connections are included. Computer facilities are also listed. The nation's regulatory policies are…
Théodoridés, J; Desportes, I; Jolivet, P
Study of 14 species of Gregarines from terrestrial arthropods (Myriapoda and Insecta) of south Korea. Some of them (Ramicephalus ozakii, Gregarina monoducta, Hoplorhynchus ozakii, Stylocephalus bahli) are typically asiatic whereas the others were already described from identical or similar european hosts.
Lee, Yanghee; Kim, Sangwon
Objective: This study explored the prevalence of childhood maltreatment in South Korea using the retrospective version of ICAST and the associations between perceptions of abuse experienced during childhood and recent interpersonal problems and depression. Methods: 539 young persons, aged 18-24 years, from various universities, work places, and…
Cho, Dongchul; Shin, Sukha
This paper examines Korea's employment dynamics and analyzes how adverse impacts could be mitigated during the recent economic crisis in comparison with the 1997 to 1998 Asian crisis. A clear lesson is that policies to mitigate adverse impacts of financial crisis on the macroeconomic level should be given priority for preserving employment. In…
The AsiaBarometer survey of 1,023 respondents shows Life in Korea is highly modernized and digitalized without being much globalized. Despite the modernization and digitalization of their lifestyles, ordinary citizens still prioritize materialistic values more than post-materialistic values, and they remain least satisfied in the material life…
...] [Pages 67912-67918] [FR Doc No: 2010-27829] DEPARTMENT OF THE TREASURY Office of Foreign Assets Control 31 CFR Part 510 North Korea Sanctions Regulations AGENCY: Office of Foreign Assets Control, Treasury. ACTION: Final rule. SUMMARY: The Department of the Treasury's Office of Foreign Assets Control...
Lim, Soo; Koo, Bo Kyeong; Lee, Eun Jung; Park, Jin Ho; Kim, Myoung Hee; Shin, Kun Hong; Ha, Yong Chan; Cho, Nam Han; Shin, Chan Soo
Osteoporosis is a major public health problem in both Western and Asian populations. Because the aged population in Korea is increasing, the number of osteoporotic fractures is thought to be also increasing. However, there has been no nationwide analysis of osteoporotic fractures in Korea. We analyzed the incidence and cost of hip fracture from 2001 to 2004 by using data from the Health Insurance Review Agency, Korea. In the over 50 years age group, the number of hip fractures in women increased from 250.9/100,000 persons in 2001 to 262.8/100,000 in 2004, a 4.7% increase. However, that in men decreased from 162.8/100,000 in 2001 to 137.5/100,000 in 2004, a 15.5% decrease. Direct medical care costs of hip fracture increased from $62,707,697 in 2001 to $65,200,035 in 2004, and the proportional cost of hip fractures in the national medical costs increased by 4.5% over 4 years (from 0.200% in 2001 to 0.209% in 2004). On analysis of the population-based data obtained from the whole country from 2001 to 2004, the incidence rate of hip fractures in women, not in men, and its cost have increased in Korea. The gender distribution of hip fractures underlines the need for aggressive intervention in osteoporosis in elderly women.
English education in Japan and Korea are similar in some respects. Although both countries are not completely but mostly monolingual societies, where citizens do not need English in their daily life, they have begun to realize the importance of English as a tool for international communication, and as a result their English education is becoming…
Kim, Gyoung Hee; Kim, Kwang-Hyung; Son, Kyeong In; Choi, Eu Ddeum; Lee, Young Sun; Jung, Jae Sung; Koh, Young Jin
A bacterial pathogen, Pseudomonas syringae pv. actinidiae (Psa), is a causal agent of kiwifruit bacterial canker worldwide. Psa biovar 3 (Psa3) was first detected in 2011 at an orchard in Dodeok-myeon, Goheunggun, Jeonnam Province in Korea. In this study, we present the results of an epidemiological study regarding Psa3 occurrence on kiwifruit orchards in Korea for the period of 2013 to 2015. Since the first detection of Psa3 in 2011, there was no further case reported by 2013. However, Psa3 was rapidly spreading to 33 orchards in 2014; except for three orchards in Sacheonsi, Gyeongnam Province, most cases were reported in Jeju Island. Entering 2015, bacterial canker by Psa3 became a pandemic in Korea, spreading to 72 orchards in Jeju Island, Jeonnam, and Gyeongnam Provinces. Our epidemiological study indicated that the first Psa3 incidence in 2011 might result from an introduction of Psa3 through imported seedlings from China in 2006. Apart from this, it was estimated that most Psa3 outbreaks from 2014 to 2015 were caused by pollens imported from New Zealand and China for artificial pollination. Most kiwifruit cultivars growing in Korea were infected with Psa3; yellow-fleshed cultivars (Yellow-king, Hort16A, Enza-gold, Zecy-gold, and Haegeum), red-fleshed cultivars (Hongyang and Enza-Red), green-fleshed cultivars (Hayward and Daeheung), and even a kiwiberry (Skinny-green). However, susceptibility to canker differed among cultivars; yellow- and red-fleshed cultivars showed much more severe symptoms compared to the green-fleshed cultivars of kiwifruit and a kiwiberry. PMID:27904461
Holmes, Edward C.
The increasing availability of complete genome sequences of RNA viruses has the potential to shed new light on fundamental aspects of their biology. Here, I use case studies of 3 RNA viruses to explore the impact of genomic sequence data, with particular emphasis on influenza A virus. Notably, the studies of RNA virus genomics undertaken to date largely focused on issues of evolution and epidemiology, and they have given these disciplines new impetus. However, genomic data have so far made fewer inroads into areas of more direct importance for disease, prevention, and control; thus, harnessing their full potential remains an important goal. PMID:19729846
Bennett, Heather; Waser, Nathalie; Johnston, Karissa; Kao, Jia-Horng; Lim, Young-Suk; Duan, Zhong-Ping; Lee, Youn-Jae; Wei, Lai; Chen, Chien-Jen; Sievert, William; Yuan, Yong; Li, Hong
Hepatitis C virus (HCV) infection is associated with substantial clinical and economic burden and is an important public health issue in Asia. The objective of this review was to characterize HCV epidemiology and related complications in China, Japan, South Korea and Taiwan. A search of electronic databases and conference abstracts identified 71 potentially relevant articles. Of those, 55 were included in the epidemiology review and 9 in the review of HCV-related complications. HCV prevalence in the general population was 1.6% in China, 0.6-0.9% in Japan, 0.6-1.1% in South Korea and 1.8-5.5% in Taiwan. Prevalence was higher for injecting drug users (48-90%) and those with human immunodeficiency virus coinfection (32-85%) and was lower for blood donors (<1%). Annual incidence of HCV in China was 6.01 per 100,000. HCV genotype 1b was associated with the highest incidence of hepatocellular carcinoma (HCC). Five-year survival for patients with liver cirrhosis was 73.8%, decreasing to 39.2% following liver transplantation; the majority of deaths were attributable to HCC. Limitations were that the majority of studies included in the epidemiology review were small, regional studies conducted in specific populations, and there was an absence of large population-based studies. Thus, estimates may not be representative of the epidemiology of HCV for each country. The prevalence HCV in China and HCV incidence in the Asian region remain largely unknown, and they are likely underestimated. Further epidemiologic and clinical data are needed to provide more precise estimates for use by public health agencies.
... International Trade Administration Large Power Transformers From the Republic of Korea: Postponement of... transformers from the Republic of Korea (Korea). See Large Power Transformers from the Republic of Korea... petitioners to the Department, entitled ``Large Power Transformers from the Republic of Korea--...
Lee, Youngdeuk; Lee, Su-Jin; Park, Gun-Hoo; Heo, Soo-Jin; Umasuthan, Navaneethaiyer; Kang, Do-Hyung; Oh, Chulhong
Gilvimarinus agarilyticus JEA5, which effectively degrades agar, was isolated from the seawater of Jeju Island, Republic of Korea. Here, we report the draft genome sequence of G. agarilyticus JEA5 with a total genome size of 4,179,438bp from 2 scaffolds (21 contigs) with 53.15% G+C content. Various polysaccharidases including 11 predicted agarases were observed from the draft genome of G. agarilyticus JEA5.
Romero-Severson, Ethan O.; Bulla, Ingo; Leitner, Thomas
Although the use of phylogenetic trees in epidemiological investigations has become commonplace, their epidemiological interpretation has not been systematically evaluated. Here, we use an HIV-1 within-host coalescent model to probabilistically evaluate transmission histories of two epidemiologically linked hosts. Previous critique of phylogenetic reconstruction has claimed that direction of transmission is difficult to infer, and that the existence of unsampled intermediary links or common sources can never be excluded. The phylogenetic relationship between the HIV populations of epidemiologically linked hosts can be classified into six types of trees, based on cladistic relationships and whether the reconstruction is consistent with the true transmission history or not. We show that the direction of transmission and whether unsampled intermediary links or common sources existed make very different predictions about expected phylogenetic relationships: (i) Direction of transmission can often be established when paraphyly exists, (ii) intermediary links can be excluded when multiple lineages were transmitted, and (iii) when the sampled individuals’ HIV populations both are monophyletic a common source was likely the origin. Inconsistent results, suggesting the wrong transmission direction, were generally rare. In addition, the expected tree topology also depends on the number of transmitted lineages, the sample size, the time of the sample relative to transmission, and how fast the diversity increases after infection. Typically, 20 or more sequences per subject give robust results. We confirm our theoretical evaluations with analyses of real transmission histories and discuss how our findings should aid in interpreting phylogenetic results. PMID:26903617
Sherman, Stephanie L.; Allen, Emily G.; Bean, Lora H.; Freeman, Sallie B.
Down syndrome (DS) is the most commonly identified genetic form of mental retardation and the leading cause of specific birth defects and medical conditions. Traditional epidemiological studies to determine the prevalence, cause, and clinical significance of the syndrome have been conducted over the last 100 years. DS has been estimated to occur…
Jenkins, C. David
Reviews epidemiological studies of cardiovascular diseases especially coronary heart disease (CHD), to document their major public health importance, changes in mortality during this century, and international comparisons of trends. Finds major risk factors for CHD are determined in large part by psychosocial and behavioral mechanisms. Asserts…
Romero-Severson, Ethan O.; Bulla, Ingo; Leitner, Thomas
The use of phylogenetic trees in epidemiological investigations has become commonplace, but their epidemiological interpretation has not been systematically evaluated. Here, we use an HIV-1 within-host coalescent model to probabilistically evaluate transmission histories of two epidemiologically linked hosts. Previous critique of phylogenetic reconstruction has claimed that direction of transmission is difficult to infer, and that the existence of unsampled intermediary links or common sources can never be excluded. The phylogenetic relationship between the HIV populations of epidemiologically linked hosts can be classified into six types of trees, based on cladistic relationships and whether the reconstruction is consistent with the true transmission history or not. We show that the direction of transmission and whether unsampled intermediary links or common sources existed make very different predictions about expected phylogenetic relationships: (i) Direction of transmission can often be established when paraphyly exists, (ii) intermediary links can be excluded when multiple lineages were transmitted, and (iii) when the sampled individuals’ HIV populations both are monophyletic a common source was likely the origin. Inconsistent results, suggesting the wrong transmission direction, were generally rare. In addition, the expected tree topology also depends on the number of transmitted lineages, the sample size, the time of the sample relative to transmission, and how fast the diversity increases after infection. Typically, 20 or more sequences per subject give robust results. Moreover, we confirm our theoretical evaluations with analyses of real transmission histories and discuss how our findings should aid in interpreting phylogenetic results.
Romero-Severson, Ethan O.; Bulla, Ingo; Leitner, Thomas
The use of phylogenetic trees in epidemiological investigations has become commonplace, but their epidemiological interpretation has not been systematically evaluated. Here, we use an HIV-1 within-host coalescent model to probabilistically evaluate transmission histories of two epidemiologically linked hosts. Previous critique of phylogenetic reconstruction has claimed that direction of transmission is difficult to infer, and that the existence of unsampled intermediary links or common sources can never be excluded. The phylogenetic relationship between the HIV populations of epidemiologically linked hosts can be classified into six types of trees, based on cladistic relationships and whether the reconstruction is consistent with the truemore » transmission history or not. We show that the direction of transmission and whether unsampled intermediary links or common sources existed make very different predictions about expected phylogenetic relationships: (i) Direction of transmission can often be established when paraphyly exists, (ii) intermediary links can be excluded when multiple lineages were transmitted, and (iii) when the sampled individuals’ HIV populations both are monophyletic a common source was likely the origin. Inconsistent results, suggesting the wrong transmission direction, were generally rare. In addition, the expected tree topology also depends on the number of transmitted lineages, the sample size, the time of the sample relative to transmission, and how fast the diversity increases after infection. Typically, 20 or more sequences per subject give robust results. Moreover, we confirm our theoretical evaluations with analyses of real transmission histories and discuss how our findings should aid in interpreting phylogenetic results.« less
Kodama, H; Ohno, Y
In this paper, urolithiasis is reviewed from the standpoint of analytical epidemiology, which examines a statistical association between a given disease and a hypothesized factor with an aim of inferring its causality. Factors incriminated epidemiologically for stone formation include age, sex, occupation, social class (level of affluence), season of the year and climate, dietary and fluid intake and genetic prodisposition. Since some of these factors are interlinked, they are broadly classified into five categories and epidemiologically looked over here. Genetic predisposition is essentially endorsed by the more frequent episodes of stone formation in the family members of stone formers, as compared to non-stone formers. Nevertheless, some environmental factors (likely to be dietary habits) shared by family members are believed to be relatively more important than genetic predisposition. A hot, sunny climate may influence stone formation through inducing dehydration with increased perspiration and increased solute concentration with decreased urine volume, coupled with inadequate liquid intake, and possibly through the greater exposure to ultraviolet radiation which eventually results in an increased vitamin D production, conceivably correlated with seasonal variation in calcium and oxalate excretion to the urine. Urinary tract infections are importantly involved in the formation of magnesium ammonium phosphate stones in particular. The association with regional water hardness is still in controversy. Excessive intake of coffee, tea and alcoholic beverages seemingly increase the risk of renal calculi, though not consistently confirmed. Many dietary elements have been suggested by numerous clinical and experimental investigations, but a few elements are substantiated by analytical epidemiological investigations. An increased ingestion of animal protein and sugar and a decreased ingestion of dietary fiber and green-yellow vegetables are linked with the higher
Parascandola, M; Weed, D
Causation is an essential concept in epidemiology, yet there is no single, clearly articulated definition for the discipline. From a systematic review of the literature, five categories can be delineated: production, necessary and sufficient, sufficient-component, counterfactual, and probabilistic. Strengths and weaknesses of these categories are examined in terms of proposed characteristics of a useful scientific definition of causation: it must be specific enough to distinguish causation from mere correlation, but not so narrow as to eliminate apparent causal phenomena from consideration. Two categories—production and counterfactual—are present in any definition of causation but are not themselves sufficient as definitions. The necessary and sufficient cause definition assumes that all causes are deterministic. The sufficient-component cause definition attempts to explain probabilistic phenomena via unknown component causes. Thus, on both of these views, heavy smoking can be cited as a cause of lung cancer only when the existence of unknown deterministic variables is assumed. The probabilistic definition, however, avoids these assumptions and appears to best fit the characteristics of a useful definition of causation. It is also concluded that the probabilistic definition is consistent with scientific and public health goals of epidemiology. In debates in the literature over these goals, proponents of epidemiology as pure science tend to favour a narrower deterministic notion of causation models while proponents of epidemiology as public health tend to favour a probabilistic view. The authors argue that a single definition of causation for the discipline should be and is consistent with both of these aims. It is concluded that a counterfactually-based probabilistic definition is more amenable to the quantitative tools of epidemiology, is consistent with both deterministic and probabilistic phenomena, and serves equally well for the acquisition and the
Rouphael, Nadine G.; Stephens, David S.
Neisseria meningitidis (the meningococcus) causes significant morbidity and mortality in children and young adults worldwide through epidemic or sporadic meningitis and/or septicemia. In this review, we describe the biology, microbiology, and epidemiology of this exclusive human pathogen. N. meningitidis is a fastidious, encapsulated, aerobic gram-negative diplococcus. Colonies are positive by the oxidase test and most strains utilize maltose. The phenotypic classification of meningococci, based on structural differences in capsular polysaccharide, lipooligosaccharide (LOS) and outer membrane proteins, is now complemented by genome sequence typing (ST). The epidemiological profile of N. meningitidis is variable in different populations and over time and virulence of the meningococcus is based on a transformable/plastic genome and expression of certain capsular polysaccharides (serogroups A, B, C, W-135, Y and X) and non-capsular antigens. N. meningitidis colonizes mucosal surfaces using a multifactorial process involving pili, twitching motility, LOS, opacity associated, and other surface proteins. Certain clonal groups have an increased capacity to gain access to the blood, evade innate immune responses, multiply, and cause systemic disease. Although new vaccines hold great promise, meningococcal infection continues to be reported in both developed and developing countries, where universal vaccine coverage is absent and antibiotic resistance increasingly more common. PMID:21993636
Chen, Yi; Brown, Eric; Knabel, Stephen J.
The purpose of this chapter is to describe the basic principles and advancements in the molecular epidemiology of foodborne pathogens. Epidemiology is the study of the distribution and determinants of infectious diseases and/or the dynamics of disease transmission. The goals of epidemiology include the identification of physical sources, routes of transmission of infectious agents, and distribution and relationships of different subgroups. Molecular epidemiology is the study of epidemiology at the molecular level. It has been defined as "a science that focuses on the contribution of potential genetic and environmental risk factors, identified at the molecular level, to the etiology, distribution and prevention of diseases within families and across populations".
Kim, Ji Han; Yim, Jae-Joon
After the Korean War (1950-1953), nearly 6.5% of South Korea's population had active tuberculosis (TB). In response, South Korea implemented the National Tuberculosis Program in 1962. From 1965 to 1995, the prevalence of bacteriologically confirmed pulmonary TB in South Korea decreased from 940 to 219 cases per 100,000 population. Astounding economic growth might have contributed to this result; however, TB incidence in South Korea remains the highest among high-income countries. The rate of decrease in TB incidence seems to have slowed over the past 15 years. A demographic shift toward an older population, many of whom have latent TB and various concurrent conditions, is challenging TB control efforts in South Korea. The increasing number of immigrants also plays a part in the prolonged battle against TB. A historical review of TB in South Korea provides an opportunity to understand national TB control efforts that are applicable to other parts of the world.
Podenas, Sigitas; Byun, Hye-Woo
Korean species of the crane fly genus Metalimnobia Matsumura, 1911 (Diptera: Limoniidae), are taxonomically revised. Metalimnobia (Metalimnobia) channpayna new species, is described and figured, M. (M.) bifasciata (Schrank, 1781), M. (M.) quadrinotata (Meigen, 1818) and M. (M.) zetterstedti (Tjeder, 1968) are listed for the first time in Korea, new information for previously known species, M. (M.) quadrimaculata (Linnaeus, 1760) is added. Identification key for all Korean Metalimnobia species is given. Wings, male and female terminalia are illustrated for all species.
42 Yi Sang-il and Chin Se-ku. Yongbyon nuclear facility can be disabled within a year. JongAng Ilbo (internet version), March 13, 2007. 43...Print Media, August 30, 3007. 46 Choe Sang- hun and David E. Sanger, North Korea claims U.S. will remove sanctions, International Herald Tribune...attempts in late 2006 through the spring of 2007 to smuggle conventional arms, including machine guns , automatic rifles, and anti-tank rocket launchers
Lee, Hye-Eun; Kang, Seong-Kyu
Objectives The extent of the occupational cancer burden has rarely been estimated in Korea. The aim of this study is to provide an estimation of the population attributable fraction (PAF) of occupational cancer in Korea. Methods Nine kinds of Group 1 carcinogens addressed by the International Agency for Research on Cancer (IARC) and 7 kinds of cancer were selected for the target carcinogens and diseases, respectively. The prevalence of carcinogen-exposed workers was estimated and correction factors were applied so that the value would be representative of the total population. Data on relative risk (RR) were taken from IARC reports and were compared with the RRs from the studies on Korean workers. The PAF was estimated according to Levin's formula. Results The proportion of the general Korean population exposed to carcinogens was 9.7%. The PAF of total cancer was 1.1% for incident cancer cases and 1.7% for cancer deaths. The PAFs of lung cancer and leukemia were 7.0% and 4.%, respectively. With the RRs reported from Korean studies, the PAF for lung cancer and leukemia were 3.7% and 3.4%, respectively. Conclusion The PAF in this study (1.1%) was lower than that reported in previous studies (2-4%) from developed countries. Considering that only 9 of the 29 kinds of Group 1 carcinogens were included in this study, the PAF might be underestimated. However, because the process of industrialization in Korea differs from that which occurred in other developed countries, 1.1% of the PAF might be appropriate for Korea. PMID:22953164
though the South Korean Navy won the battle in the Yellow Sea, Kim Dae-Jung fired the fleet commander, Admiral Park Jung- seung , because North Korea...during the administration of President Kim Dae-jung and continued for 10 years through the Roh Moo-hyun Administration. This unilateral policy was based...changed during the administration of President Kim Dae-jung and continued for 10 years through the Roh Moo-hyun Administration. This unilateral policy
Son, Soon-Hwan; Lee, Sook-Kyung; Kim, Kwang-Sin
Four CANDU reactors have been operating at the site of Wolsong Nuclear Power Generation in Korea. The Wolsong tritium removal facility was constructed to reduce the tritium levels in heavy water systems. This facility was designed to process 100kg/h of tritiated heavy water feed and to produce 99% pure T(2). This recovered tritium will be made available for commercial applications. The initial phases on the tritium applications are made to establish the infrastructure and the tritium controls.
prevent North Korea from provoking a war. 80 “Singapore’s Lee calls N. Koreans ‘ psychopathic ...Singapores-Lee-calls-NKoreans- psychopathic ---WikiLeaks. 44 Before continuing, let us clarify the term “collapse.” As Samuel Kim states, “The...Singapore’s Lee calls N. Koreans ‘ psychopathic ’—WikiLeaks,” Agence France-Press, November 30, 2010. Accessed January 12, 2011. http
Lee, Seung-Kyu; Park, Hyeon-Soo
Objectives Despite the great contribution made by chemical substances to the development of modern civilization, their indiscriminate use has caused various kinds of damage to the global environment and human beings. Accordingly, the major developed countries and international society have tried to ensure the safe use of chemicals and a reduction in the use of hazardous chemicals through the establishment of the United Nations Environment Programme and various international agreements. In this reason, we tried to introduce about Green Chemistry progress at the present in worldwide and Korea. Methods We checked and analyzed relative journals, reports using keyword as like Green Chemistry, alternative chemicals, eco-friendly etc. and major country’s government homepage search. Results Green Chemistry theory, which argues for the reduction or removal of harmfulness in chemicals throughout their entire life-cycle, has been spreading, and major developed countries, such as the US and Denmark, have developed and operate programs to provide reliable chemical information to help replace hazardous chemicals. Korea has also been conducting studies as like eco-innovation project. Through this project the “Alternative Chemical Search program,” has been developed, distributed, and operated since 2011 to provide reliable information to small and medium-sized businesses that have difficulties collecting information to ensure conformity to international regulations. The program provides information that includes the regulations of major countries and Korea, information on 340 alternative chemicals, 70 application cases, and 1:1 consulting. Conclusions The Alternative Chemical Search program is expected to contribute to the establishment of response systems for regulation of Korean small and medium-sized businesses, and it also will be used to provide basic data for Korean hazardous chemical regulation, together with the Act on the Registration and Evaluation, etc. of
2015 joint statement on North Korea says, “The United States will continue to strongly support [President Park’s] vision of a peacefully unified Korean...around the year 2020 . 51 The city of Dongducheon, where those soldiers are based, has protested this decision and withdrawn some cooperation with the...munitions, and ISR (intelligence, surveillance, and reconnaissance) assets. Reportedly, the Opcon transfer may not occur until 2020 or later. 67
plan B,” Asia Tiimes, May 21, 2009, Online edition. 2 The extent that Pyongyang has...Mother Jones, Vol. 28, No. 3, May 1, 2003. p. 52. 42 Food and Agriculture Organization. Food Security Statistics. Online at http://www.fao.org...for Military.” People’s Daily Online , April 12, 2005. 64 Asia: The deal that wasn’t; North Korea. The Economist. London: September 24, 2005. p. 81
authorities in Myanmar who believed that local insurgent groups were intent on trading heroin for the arms.21 North Korea has also used its diplomatic...represent another strategic dimension of threats emanating from North Korea . While most of the world is focused on the country’s nuclear weapons and...incident, groups in Myanmar do not earn their profits from street sales, but from the middleman that has been, in certain instances, North Korea . Acting
members on a state visit to Rangoon, Burma . In 1987 North Korea shot down a Korean Air Lines commercial flight.9 Besides the North Korean threat, South...arrivals of North Korean defectors ................................................37 Figure 4. Anti-terrorism-related organizations in Korea after 9.11...study will determine whether current Korean anti-terrorism programs effectively address all terrorist threats, including threats from North Korea
Bush Administration in 2008 committed 500,000 tons of foodgrains.. South Korea followed a conciliation policy toward North Korea under the...dollars in foreign exchange earnings since 1998 to import food or medicines . The regime has not adopted agricultural reforms similar to those of... conciliation policy were: the extension of South Korean economic and humanitarian aid to North Korea, the promotion of North-South economic relations
South Korea by the United States. 41 During the war, the United Nations set up the Civilian Relief Agency to provide medicine, food , and shelter to...Japanese coast. Their mission was to escort and protect vessels carrying food , oil and other resources to Japan along two sea lanes, one connecting...Sales credits to South Korea for FY 87 to $230 mlllion.l II Security Assistance to the Republic of Korea has been instrumental in perserving peace In the
between 30 and 50 kilograms, enough for five to eight atomic weapons. After North Korea tested a nuclear device in October 2006, the six party talks...the plutonium reprocessing plant produced enough weapons grade plutonium for the production of several atomic bombs. North Korea tested an atomic...produces and tests atomic bombs, and the locations where North Korea stores plutonium and atomic bombs. The declaration also reportedly contains no
negotiation the questions of the withdrawal of all foreign forces from Korea , the peaceful settlement of the Korean question, etc.5 Both sides did meet in...invasion]." The Republic of Korea faced an insurgency and guerilla warfare that followed the Maoist model and culminated in the North Korean Army...the United States through a proxy. 12 . The first year of the war saw four major shifts in momentum. First, the DPRK (or North Korea ) thrust its Korean
precepts to Korea as early as 1936 when he wrote, "If the Koreans wish to break away from the claims of Japanese [read American] imperi- alism, we will... Korea . Both actions .Vcre preceded by the White Paper and Secretary of State Dean Acheson’s public statements that delineated an American defensive ...predictably denounced the American action in Korea , but did so in a manner that indicated little concern over Korean events. What shocked and incensed
is likely in Korea . Some argue that the Korean economy would have developed much faster without the burden of the defense spending. We could have...industry to the civilian industry in Korea . The intent of this study is to determine how much impact and influence the Korean defense industry has had...in Korea based on 1987 data. Dr. Dong J. Hwang studied the future of the Korean defense industry. But none of these authors studied the defense
Kwak, The Reduction of US Forces in Korea in the Inter- Korean Peace Process: The Korean Journal of Defense Analysis, Vol. II No. 2 Winter 1990, pp... Korean Peace Process: The Korean Journal of Defense Analysis, Vol. II No. 2 Winter 1990. 11. Levin, Norman D., and Richard L. Sneider, " Korea in...group with 500 officers and enlisted personnel. After the Korean war broke out in June 1950, the United States sent its troops to Korea in July under
is becoming politically less viable.”4 In the Korean theater of operations (KTO), Republic of Korea (ROK) and U.S. plan- ners, from Combined Forces...in the Korean War. —Lieutenant General Walton H. Walker, Commander, 8th U.S. Army, Korea , 19501 South Korean military members participate with U.S...pallet buildup and cargo loading Supplies are loaded onto Korean C–130 at Hickam Air Base, Hawaii Republic of Korea air force security advisor speaks
Cha, Eun Shil; Khang, Young-Ho; Lee, Won Jin
Pesticide poisoning has been recognized as an important public health issue around the world. The objectives of this study were to report nationally representative figures on mortality from and the incidence of pesticide poisoning in South Korea and to describe their epidemiologic characteristics. We calculated the age-standardized rates of mortality from and the incidence of pesticide poisoning in South Korea by gender and region from 2006 through 2010 using registered death data obtained from Statistics Korea and national healthcare utilization data obtained from the National Health Insurance Review and Assessment Service of South Korea. During the study period of 2006 through 2010, a total of 16,161 deaths and 45,291 patients related to pesticide poisoning were identified, marking respective mortality and incidence rates of 5.35 and 15.37 per 100,000 population. Intentional self-poisoning was identified as the major cause of death due to pesticides (85.9%) and accounted for 20.8% of all recorded suicides. The rates of mortality due to and incidence of pesticide poisoning were higher in rural than in urban areas, and this rural-urban discrepancy was more pronounced for mortality than for incidence. Both the rate of mortality due to pesticide poisoning and its incidence rate increased with age and were higher among men than women. This study provides the magnitude and epidemiologic characteristics for mortality from and the incidence of pesticide poisoning at the national level, and strongly suggests the need for further efforts to prevent pesticide self-poisonings, especially in rural areas in South Korea.
Westrin, C G; Nilstun, T; Smedby, B; Haglund, B
To an increasing extent ethical controversies affect and sometimes obstruct public health work and epidemiological research. In order to improve communication between the concerned parties a model for identification and analysis of ethical conflicts in individual-based research has been worked out in co-operation between epidemiologists and moral philosophers. The model has two dimensions. One dimension specifies relevant ethical principles (as beneficence, non-maleficence, autonomy and justice). The other dimension specifies the groups of persons involved in the conflict under consideration (for example: the study-population, individuals who may benefit from the results, the researchers and their personnel, the community at large). The model has been applied to the problem of legitimacy of case-register research and to problems in psychiatric health services research as well as epidemiological research. PMID:1460647
Chad, the land located in Central Africa nowadays is one of the poorest countries in the world, what is connected with catastrophic demographic indicators and numerous cases of infectious diseases among local population as well as external and internal refugees. Epidemiologic profile is dominated by vector-, water-, food-borne, respiratory, and sexually transmitted diseases. Environmental factors, such as an effect of high temperature, sand and dust storms also pose essential threat. This is related to location of majority of Chad territory in the area of Sahara and Sahel. The article presents information concerning current epidemiological hazards encountered by visitors in this country. This knowledge is essential for Polish health service and armed forces in the context of forming of EUFOR mission in Chad with participation of our soldiers.
Marley, Andrew R; Nan, Hongmei
Colorectal cancer is currently the third deadliest cancer in the United States and will claim an estimated 49,190 U.S. lives in 2016. The purpose of this review is to summarize our current understanding of this disease, based on nationally published statistics and information presented in peer-reviewed journal articles. Specifically, this review will cover the following topics: descriptive epidemiology (including time and disease trends both in the United States and abroad), risk factors (environmental, genetic, and gene-environment interactions), screening, prevention and control, and treatment. Landmark discoveries in colorectal cancer risk factor research will also be presented. Based on the information reviewed for this report, we suggest that future U.S. public health efforts aim to increase colorectal cancer screening among African American communities, and that future worldwide colorectal cancer epidemiology studies should focus on researching nutrient-gene interactions towards the goal of improving personalized treatment and prevention strategies. PMID:27766137
Kim, Yong Soo; Choi, Yong Jun
This study aimed to describe the ecology of medical care in Korea. Using the yearly data of 2012 derived from the Korea Health Panel, we estimated the numbers of people per 1,000 residents aged 18 and over who had any health problem and/or any medical care at a variety of care settings, such as clinics, hospitals, and tertiary hospitals, in an average month. There was a total of 11,518 persons in the study population. While the number of those who had any health problem in an average month was estimated to be 939 per 1,000 persons, the estimated numbers of ambulatory care users were 333 at clinics, 101 at hospital outpatient departments, 35 at tertiary hospital outpatient departments, and 38 for Korean Oriental medical providers. The number of people who used emergency care at least once was 7 per 1,000 persons in an average month. The numbers of people hospitalized in clinics and hospitals were 3 and 8, respectively, while 3 persons were admitted to tertiary hospitals. There was a gap between the number of people experiencing any health problem and that of those having any medical care, and primary care comprised a large share of people's medical care experiences. It was noteworthy that more patients received ambulatory care at tertiary hospitals in Korea than in other countries. We hope that discussion about care delivery system reform and further studies will be encouraged.
Particularly geared to physicians and cancer researchers, this study of the epidemiology and etiology of leukemia analyzes the four major leukemia subtypes in terms of genetic and familial determinant factors and examines the incidence, distribution and frequency of reported leukemia clusters. Linet discusses the connection between other types of malignancies, their treatments, and the subsequent development of leukemia and evaluates the impact on leukemia onset of such environmental factors as radiation therapy, drugs, and occupational hazards.
Coon, W W
This review of the epidemiology of venous thromboembolism includes estimates of incidence and prevalence of venous thrombosis and its sequelae, a discussion geographical, annual and seasonal variations and data concerning possible risk factors. Selection of patients at increased risk for development of deep venous thrombosis or pulmonary embolism for specific diagnostic screening or for prophylactic therapy with low-dose heparin may be a more effective approach to lowering morbidity and mortality from this disease. PMID:329779
Abramovici, S; Bagić, A
Modern epidemiology of epilepsy maximizes the benefits of advanced diagnostic methods and sophisticated techniques for case ascertainment in order to increase the diagnostic accuracy and representativeness of the cases and cohorts studied, resulting in better comparability of similarly performed studies. Overall, these advanced epidemiologic methods are expected to yield a better understanding of diverse risk factors, high-risk populations, seizure triggers, multiple and poorly understood causes of epilepsy, including the increasing and complex role of genetics, and establish the natural course of treated and untreated epilepsy and syndromes - all of which form the foundation of an attempt to prevent epileptogenesis as the primary prophylaxis of epilepsy. Although data collection continues to improve, epidemiologists still need to overcome definition and coding variability, insufficient documentation, as well as the interplay of socioeconomic factors and stigma. As most of the 65-70 million people with epilepsy live outside of resource-rich countries, extensive underdiagnosis, misdiagnosis, and undertreatment are likely. Epidemiology will continue to provide the necessary information to the medical community, public, and regulators as the foundation for improved health policies, targeted education, and advanced measures of prevention and prognostication of the most common severe brain disorder.
Picq, J J; Roux, J
Schistosomiasis are, with three hundred million of infested people, the second world endemy, after malaria. For each of the four species, the distribution areas, the life cycle and the main epidemiological features are recalled in the first chapter. In the five following chapters, the authors consider the human or animal reservoirs of virus, the importance of these diseases towards public health, the gasteropod molluscs acting as intermediate hosts, and the problems of immunity in man. The concepts of "schistosomian infection" and "schistosomian disease" are exposed as well as the differences affecting the various strains of schistosomes and snails intermediate hosts. The authors emphasize the value of quantitative parasitological techniques and sero-immunological methods for epidemiological surveys. They underline the difficulties met in the evaluation of the effect of these diseases upon public health. The main causes inducing the duration of the endemy and those responsible for its extension are studied. The value of mathematic patterns is briefly discussed. Quantitative data compiled through epidemiological surveys should improve the use of the various means presently available for controling schistosomiasis.
Kim, H-R; Kwon, Y-K; Bae, Y-C; Oem, J-K; Lee, O-S
In South Korea, 32 sequences of chicken infectious anemia virus (CIAV) from various flocks of breeder and commercial chickens were genetically characterized for the first time. Phylogenetic analysis of the viral protein 1 gene, including a hypervariable region of the CIAV genome, indicated that Korean CIAV strains were separated into groups II, IIIa, and IIIb. Strains were commonly identified in great-grandparent and grandparent breeder farms as well as commercial chicken farms. In the field, CIAV strains from breeder farms had no clinical effects, but commercial farm strains were associated with depression, growth retardation, and anemia regardless of the group from which the strain originated. In addition, we identified 7 CIAV genomes that were similar to vaccine strains from vaccinated and unvaccinated breeder flocks. These data suggest that further studies on pathogenicity and vaccine efficacy against the different CIAV group are needed, along with continuous CIAV surveillance and genetic analysis at breeder farms.
Kim, Sang Guk; Yang, Seung Won; Jang, An Soo; Seo, Jeong Pyeong; Han, Sang Woo; Yeom, Chung Ho; Kim, Yong Chul; Oh, Sung Hee; Kim, Jung Seok; Nam, Hae Sung; Chung, Dong Jin; Chung, Min Young
Background: Ethnic and geographic differences exist in the prevalence of diabetes mellitus which has increased dramatically in South Korea. A few community-based epidemiologic studies with oral glucose tolerance test were performed in South Korea. The purpose of this study was to determine the prevalence of diabetes mellitus by the World Health Organization (WHO) and the American Diabetic Association (ADA) diagnostic criteria and to investigate their associated risk factors. Also, we compared and analyzed the characteristics of Koreans by WHO and ADA diagnostic criteria. Methods : Between March 22, 1999 and July 14, 1999, a random sampling of 1,445 residents over 40 years of age in five villages (3 myons and 2 dongs) in Namwon City, Chollabuk-do Province, South Korea was carried out. WHO and ADA diagnostic criteria were used for the prevalence of DM, IGT and IPG. The associated factors of subjects were analyzed. Results : After age adjustment for the population projection of Korea (1999), the prevalence of DM and IGT was 13.7% and 13.8%, respectively, by WHO criteria, while the prevalence of DM, IGT and IFG was 15.8%, 12.8% and 5.7%, respectively, by ADA criteria, and the previous diagnosed diabetics were 5.8% in 665 adults over 40 years of age in the Namwon area. The age-adjusted prevalence of previously diagnosed diabetics was 5.8%. When the subjects classified by both criteria were compared, the level of agreement between WHO and ADA diagnostic criteria, except IFG, was very high (κ=0.94; p<0.001). The ROC curve analysis determined FSG of 114.5 mg/dL (6.4 mmol/L) to yield optimal sensitivity and specificity corresponding to a PP2SG 200 mg/dL (11.1 mmol/L). The prevalence of DM and IGT with ADA diagnostic criteria rose with increasing age (p<0.05). The body mass index was mean 23.8±3.4 in all the subjects, 23.75±3.46 in NGT group and 23.67±3.16 in DM group, but the differences in the prevalence of DM, IGT and IFG by BMI were not significant. The prevalence of
Lee, EunJung; Kim, Eun-Ju; Kim, Bo-Hye; Song, Jae-Young; Cho, In-Soo; Shin, Yeun-Kyung
Canine influenza A virus (CIV) causes a respiratory disease among dog populations and is prevalent in North America and Asia. Recently, Asian H3N2 CIV infection has been of particular concern, with recent reports related to reassortants with pandemic 2009 strains, direct transmission from a human H3N2, a possibility of H3N2 CIV transmission to other mammals, and even the first outbreak of H3N2 CIVs in North America in April 2015. However, despite these global concerns, our understanding of how influenza A virus transmission impacts the overall populations of H3N2 CIVs remains incomplete. Hence, we investigated the evolutionary history of the most recent two Korean CIV isolates, A/canine/Korea/BD-1/2013 and A/canine/Korea/DG1/2014, along with 57 worldwide CIVs, using comprehensive molecular analyses based on genomic genotyping. This study presents that the new Korean CIV isolates are closely related to the predominantly circulating H3N2 CIVs with genotypes K, G, E, 3B, F, 2D, F, and 1E, carrying several mutations in antigenic and host determinant sites. Also, our findings show that the genome-wide genetic variations within the H3N2 CIVs are low; however, two antigenic protein (HA and NA) analysis demonstrates genetic diversification of the H3N2 CIVs, which evolves independently between Korea and China.
Kim, Mi-Kyeong; Seo, Jang-Kyun; Kwak, Hae-Ryun; Kim, Jeong-Soo; Kim, Kook-Hyung; Cha, Byeong-Jin; Choi, Hong-Soo
Studying genetic structure and diversity of viruses is important to understand the evolutionary mechanisms that generate and maintain variations in viral populations. Cucumber mosaic virus (CMV) is endemic in most pepper fields in Korea. Currently, no effective methods for control of CMV are available due to many environmental and biological factors such as the extensive evolutionary capacity of CMV. Thus, analyzing the genetic structure of CMV populations may facilitate the development of strategies for the control of CMV. In this study, 252 pepper (Capsicum annuum) samples showing virus symptoms were collected by field surveys performed throughout Korea in 2007. Reverse-transcription polymerase chain reaction analyses revealed that, in total, 165 collected samples were infected with CMV. Forty-five CMV isolates were randomly selected within each regional subpopulation and analyzed by full-genome sequencing. Analyses of genetic diversity showed that the 2b gene of CMV is under weaker purifying selection than the other genes. Based on the phylogenetic analysis of RNA1, the CMV isolates from pepper were divided into three clusters in subgroup I. Our full-genome sequence-based molecular analyses of the CMV Korean population suggest that the subpopulations of CMV have been geographically localized in pepper fields in Korea.
Kim, Sue Hoon; Oh, Sung; Oh, Tae-Kyun; Park, Jae Sung; Kim, Sei Chang; Kim, Seong Hwan; Kim, Young Shik; Hong, Jeum Kyu; Sim, Sang-Yun; Park, Kwon Seo; Lee, Hwan Gu; Kim, Kyung Jae; Choi, Chang Won
Epidemic outbreaks of Tomato yellow leaf curl virus (TYLCV) diseases occurred in greenhouse grown tomato (Solanum lycopersicum) plants of Busan (TYLCV-Bus), Boseong (TYLCV-Bos), Hwaseong (TYLCV-Hwas), Jeju Island (TYLCV-Jeju), and Nonsan (TYLCV-Nons) in Korea during 2008-2009. Tomato disease by TYLCV has never occurred in Korea before. We synthesized the full-length genomes of each TYLCV isolate from the tomato plants collected at each area and determined their nucleotides (nt) sequences and deduced the amino acids of six open reading frames in the genomes. TYLCV-Bus and -Bos genomes shared higher nt identities with four Japanese isolates -Ng, -Omu, -Mis, and -Miy. On the other hand, TYLCV-Hwas, -Jeju, and -Nons genomes shared higher nt identities with five Chinese isolates TYLCV-AH1, -ZJ3, -ZJHZ12, -SH2, -Sh10, and two Japanese isolates -Han and -Tosa. On the basis of a neighbor-joining tree, five Korean TYLCV isolates were separated into three clades. TYLCV-Bus and -Bos formed the first clade, clustering with four Japanese isolates TYLCV-Mis, -Omu, -Ng, and -Miy. TYLCV-Jeju and -Nons formed the second clade, clustering with two Chinese isolates -ZJHZ212 and -Sh10. TYLCV-Hwas was clustered with two Japanese isolates -Han and -Tosa and three Chinese isolates -AH1, -ZJ3, and -SH2. Two fragments that had a potentially recombinant origin were identified using the RDP, GENECONV, BootScan, MaxChi, Chimaera, SiScan, and 3Seq methods implemented in RDP3.41. On the basis of RDP analysis, all TYLCV isolates could originated from the interspecies recombination between TYLCV-Mld[PT] isolated from Portugal as a major parent and TYLCTHV-MM isolated from Myanmar as a minor parent.
Ladd-Acosta, Christine; Fallin, M Daniele
Epidemiology is the branch of science that investigates the causes and distribution of disease in populations in order to provide preventative measures and promote human health. The fields of genetic and environmental epidemiology primarily seek to identify genetic and environmental risk factors for disease, respectively. Epigenetics is emerging as an important piece of molecular data to include in these studies because it can provide mechanistic insights into genetic and environmental risk factors for disease, identify potential intervention targets, provide biomarkers of exposure, illuminate gene-environment interactions and help localize disease-relevant genomic regions. Here, we describe the importance of including epigenetics in genetic and environmental epidemiology studies, provide a conceptual framework when considering epigenetic data in population-based studies and touch upon the many challenges that lie ahead.
Jeong, Seok Hoon; Kim, Han-Sung; Kim, Jae-Seok; Shin, Dong Hoon; Kim, Hyun Soo; Park, Min-Jeong; Shin, Saeam; Hong, Jun Sung; Lee, Seung Soon
Background The emergence of carbapenemase-producing Enterobacteriaceae (CPE) represents a major clinical problem because these bacteria are resistant to most antibiotics. CPE remain relatively uncommon in Korea. We report the prevalence, clinical characteristics, and molecular epidemiology of CPE isolates collected from five university hospitals in Korea. Methods Between January and December 2015, 393 non-duplicated isolates that were nonsusceptible to ertapenem were analyzed. Production of carbapenemase, extended-spectrum β-lactamase, and AmpC β-lactamase was determined by genotypic tests. Antimicrobial susceptibility profiles were determined by using an Etest. Clonality of Klebsiella pneumoniae carbapenemase (KPC)-2-producing and oxacillinase (OXA)-232-producing Klebsiella pneumoniae isolates was determined by pulsed-field gel electrophoresis (PFGE). Results Of the 393 isolates tested, 79 (20.1%) were CPE. Of these 79 isolates, 47 (59.5%) harbored the blaOXA-232 gene while the remaining isolates carried genes blaKPC-2 (n=27), blaIMP-1 (n=4), and blaNDM-1 (n=1). Among the 24 KPC-2 K. pneumoniae isolates from hospital B, 100% were resistant to carbapenems, 8% to colistin, and 0% to tigecycline. Among the 45 OXA-232 K. pneumoniae at hospital C, 95% were resistant to ertapenem, 68% to imipenem, 95% to meropenem, 10% to colistin, and 24% to tigecycline. PFGE analysis revealed a unique pattern for KPC-2 K. pneumoniae and identified 30 isolates belonging to the dominant pulsotypes (PT)1 and PT2 among 41 OXA-232 K. pneumoniae isolates. Conclusions CPE strains are present in Korea, with the majority of K. pneumoniae isolates producing OXA-232 and KPC-2. The prevalence and predominant genotypes of CPE show hospital-specific differences. PMID:27578505
Takakuwa, Tetsuya; Hongyo, Tadashi; Yang, Woo-Ick
Nasal NK/T-cell lymphoma (NKTCL) is an uncommon disease, but usually shows a highly aggressive clinical course. The disease is much more frequent in Asian and Latin American countries than in Western countries, and is universally associated with Epstein–Barr virus (EBV) infection. Analyses of gene mutations, especially p53 and c-KIT, revealed the different frequencies by district. Epidemiological studies revealed the changes of the disease frequency in Korea during the period from 1977–1989 to 1990–1996. Case-control study showed that the exposure to pesticides and chemical solvents could be causative of NKTCL. Further studies including HLA antigen typing of patients is necessary to further clarify the disease mechanism. PMID:18256789
Park, Jae-Hak; Novilla, Meliton N.; Song, Juha; Kim, Kyung-Sul; Chang, Seo-Na; Han, Ju-Hee; Lee, Byung Hee; Lee, Do-Hun; Kim, Hyun-Mac; Kim, Young-Ha; Youn, Hee-Jeong; Kil, Jihyon
This study reports the first case of Capillaria hepatica infection in a nutria in Korea. Ten nutrias, captured near the Nakdong River, were submitted to our laboratory for necropsy. White-yellowish nodules were found in the liver of 1 of the nutrias at necropsy. Histologically, the lesions were granulomatous, and infiltrations of lipid-laden macrophages, eosinophils, and several multinucleated giant cells were observed. The lesions consisted of numerous eggs and necrotic hepatocytes. The eggs were lemon-shaped and had polar plugs at the ends of both long sides. The eggs were morphologically identified as those of C. hepatica. Worldwide, C. hepatica infection in nutrias is very rare. Nutrias are a kind of livestock, as well as wildlife; therefore, an epidemiological study for parasitic infections needs to be conducted. PMID:25352702
Park, Cheol Whee
With worldwide epidemic of diabetes mellitus, diabetic nephropathy which is one of the major causes of microvascular complication has become a serious concern in Korea as well as the rest of the world. In view of its significance, there is an urgent and paramount need for proper managements that could either deter or slow the progression of diabetic nephropathy. Despite advances in care, ever increasing number of patients suffering from diabetic kidney disease and from end-stage renal disease implies that the current management is not adequate in many aspects. The reasons for these inadequacies compromise lack of early diagnosis, failure to intervene with timely and aggressive manner, and lack of understanding on the kind of interventions required. Another issue equally important for the adequate care of patients with diabetic nephropathy is an understanding of past, present and future epidemiology of diabetic nephropathy which serves, especially in Korea, as a material determining standard diagnosis and treatment and a national health-policy decision.
Elliott, Briony; Androga, Grace O; Knight, Daniel R; Riley, Thomas V
Over the recent decades, Clostridium difficile infection (CDI) has emerged as a global public health threat. Despite growing attention, C. difficile remains a poorly understood pathogen, however, the exquisite sensitivity offered by next generation sequencing (NGS) technology has enabled analysis of the genome of C. difficile, giving us access to massive genomic data on factors such as virulence, evolution, and genetic relatedness within C. difficile groups. NGS has also demonstrated excellence in investigations of outbreaks and disease transmission, in both small and large-scale applications. This review summarizes the molecular epidemiology, evolution, and phylogeny of C. difficile, one of the most important pathogens worldwide in the current antibiotic resistance era.
Lee, Seo-Young; Jung, Ki-Young; Lee, Il Keun; Yi, Sang Do; Cho, Yong Won; Kim, Dong Wook; Hwang, Seung-Sik; Kim, Sejin
The Korean national health security system covers the entire population and all medical facilities. We aimed to estimate epilepsy prevalence, anticonvulsant utilization pattern and the cost. We identified prevalent epilepsy patients by the prescription of anticonvulsants under the diagnostic codes suggesting seizure or epilepsy from 2007 Korean National Health Insurance databases. The information of demography, residential area, the kind of medical security service reflecting economic status, anticonvulsants, and the costs was extracted. The overall prevalence of treated epilepsy patients was 2.41/1,000, and higher for men than women. The age-specific prevalence was the lowest in those in their thirties and forties. Epilepsy was more prevalent among lower-income individuals receiving medical aid. The regional prevalence was the highest in Jeju Island and lowest in Ulsan city. New anticonvulsants were more frequently used than old anticonvulsants in the younger age group. The total annual cost of epilepsy or seizure reached 0.46% of total medical expenditure and 0.27% of total expenditure on health. This is the first nationwide epidemiological report issued on epilepsy in Korea. Epilepsy prevalence in Korea is comparable to those in developed countries. Economic status and geography affect the prevalence of epilepsy.
Hwang, In-Yeong; Park, Eun-Hee; Park, Yon-Koung; Park, Sun-Hee; Sung, Gyung-Hye; Park, Hye-Young; Lee, Young-Choon
Legionella pneumophila is the major causes of legionellosis worldwide. The distribution of L. pneumophila was investigated in water systems of public facilities in Busan, South Korea during 2007 and 2013-2014. L. pneumophila was isolated from 8.3% of 3,055 samples, of which the highest isolation rate (49%) was from ships and the lowest 4% from fountains. Serogroups of L. pneumophila isolated in 2007 were distributed among serogroups (sgs) 1-7 with the exception of sg 4, while those of isolates during 2013 and 2014 included also 11 sgs ( 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 15). L. pneumophila sg 1 was predominated among isolates from fountains (75%), hotels (60%), buildings (44%), hospitals (38%), and public baths (37%), whereas sg 3 and sg 7 was the most prevalent from ships (46%) and factories (40%), respectively. The predominated serogroup of L. pneumophila isolates from hot and cooling tower water was sg 1 (35% and 46%, respectively), while from cold water was sg 3 (29%). These results should be useful for epidemiological surveys to identify sources of outbreaks of legionellosis in Busan, South Korea.
Chai, Jong-Yil; Jung, Bong-Kwang; Kim, Deok-Gyu; Kim, Jae-Lip; Lim, Hyemi; Shin, Eun-Hee; Lee, Keon Hoon; Kim, Mok Ryeon; Han, Sun Jin; Yeom, Jae Hyun; Park, Sun Mi; Hwang, Jae-Sun
We conducted an epidemiological survey to determine the status of heterophyid fluke infections among people residing along the Boseong River, Gokseong-gun, South Korea (= Korea) from October 2011 to February 2012. Fecal specimens were collected from 115 (male 51, female 64) people and examined for intestinal helminth eggs using the Kato-Katz thick smear technique. The eggs of Metagonimus yokogawai together with other Metagonimus spp. were detected in 28 (24.3%) cases. Eleven egg positive people were treated with 10mg/kg praziquantel followed by MgSO4 purging in order to recover the adult flukes. Whole consecutive diarrheic stools were collected individually 4-5 times. Adult flukes recovered were 66,499 specimens (6045.4/positive case) of M. yokogawai, 343 (38.1) of Metagonimus miyatai, 3293 (299.4) of Metagonimus takahashii, 81 (20.3) of Heterophyes nocens, 6 (3.0) of Heterophyopsis continua, and 1 (1.0) of Stictodora fuscata. The results indicated that the surveyed area is a highly endemic area of metagonimiasis (three Metagonimus species) with low-grade mixed infections of 3 other heterophyid flukes. The infected people experienced variable degrees of gastrointestinal discomfort and indigestion. They consumed raw freshwater and brackish water fish, including sweetfish and mullets. It is strongly recommended that people residing in the survey area avoid eating raw fish to prevent M. yokogawai and other heterophyid infections.
Goo, Youn-Kyoung; Shin, Won-Sik; Yang, Hye-Won; Joo, So-Young; Song, Su-Min; Ryu, Jae-Sook; Lee, Won-Myung; Kong, Hyun-Hee; Lee, Won-Ki; Lee, Sang-Eun; Lee, Won-Ja; Chung, Dong-Il; Hong, Yeonchul
This study explored epidemiological trends in trichomoniasis in Daegu, South Korea. Wet mount microscopy, PCR, and multiplex PCR were used to test for Trichomonas vaginalis in vaginal swab samples obtained from 621 women visiting 2 clinics in Daegu. Of the 621 women tested, microscopy detected T. vaginalis in 4 (0.6%) patients, PCR detected T. vaginalis in 19 (3.0%) patients, and multiplex PCR detected T. vaginalis in 12 (1.9%) patients. Testing via PCR demonstrated high sensitivity and high negative predictive value for T. vaginalis. Among the 19 women who tested positive for T. vaginalis according to PCR, 94.7% (18/19) reported vaginal signs and symptoms. Notably, more than 50% of T. vaginalis infections occurred in females younger than 30 years old, and 58% were unmarried. Multiplex PCR, which simultaneously detects pathogens from various sexually transmitted infections, revealed that 91.7% (11/12) of patients were infected with 2 or more pathogens. Mycoplasma hominis was the most prevalent co-infection pathogen with T. vaginalis, followed by Ureaplasma urealyticum and Chlamydia trachomatis. Our results indicate that PCR and multiplex PCR are the most sensitive tools for T. vaginalis diagnosis, rather than microscopy which has been routinely used to detect T. vaginalis infections in South Korea. Therefore, clinicians should take note of the high prevalence of T. vaginalis infections among adolescent and young women in order to prevent persistent infection and transmission of this disease.
Lyoo, Kwang-Soo; Kim, Doo; Jang, Hyung Gwan; Lee, Seung-Joon; Park, Mi Yeoun; Hahn, Tae-Wook
Coxiella burnetii is a zoonotic agent and causes coxiellosis, which is a cause of reproductive failure in a range of animal species, including abortion and stillbirth and Q fever, which is most often characterized by an acute flu-like illness, mild pneumonia, and/or hepatitis in humans. While livestock are well recognized worldwide as a source of infection, the zoonotic risk of C. burnetii infection in companion animals such as dogs may be overlooked. For serological diagnosis, indirect immunofluorescent assay (IFA) and enzyme-linked immunosorbent assay (ELISA) are generally considered good methods for prevalence surveys of coxiellosis. In this study, we conducted a nationwide survey of the seroprevalence of previous exposure to C. burnetii in dogs, dairy cattle, and Korean native cattle (a primarily beef breed) in South Korea. Serum samples obtained from 3087 Korean native cattle, 1224 dairy cattle, and 1023 dogs were collected from eight provinces in South Korea, and IFA and ELISA were performed to test for seropositivity. The prevalence of C. burnetii was 1.7% in Korean native cattle, 10.5% in dairy cattle, and 2.9% in dogs. This is the first report identifying previous exposure to C. burnetii in South Korean dogs. Furthermore, the presence of C. burnetii antibodies in companion and feral dogs indicates that dogs can be a potential reservoir species for zoonotic risk of C. burnetii infection in South Korea. Therefore, more detailed studies aiming to clarify epidemiological factors should be performed in the future.
Setyobudi, Eko; Jeon, Chan-Hyeok; Choi, Kwangho; Lee, Sung Il; Lee, Chung Il; Kim, Jeong-Ho
The occurrence of Genus Anisakis nematode larvae in marine fishes and cephalopods is epidemiologically important because Anisakis simplex larval stage can cause a clinical disease in humans when infected hosts are consumed raw. Common squid ( Todarodes pacificus) from Korean waters were investigated for anisakid nematodes infection during 2009˜2011. In total, 1,556 larvae were collected from 615 common squids and 732 of them were subsequently identified by PCR-RFLP analysis of ITS rDNA. Depending on the sampling locations, the nematode larvae from common squid showed different prevalence, intensity and species distribution. A high prevalence (P) and mean intensity (MI) of infection were observed in the Yellow Sea (n = 250, P = 86.0%, MI = 5.99 larvae/host) and the southern sea of Korea (n = 126, P = 57.1%, MI = 3.36 larvae/host). Anisakis pegreffii was dominantly found in common squid from the southern sea (127/ 140, 90.7%) and the Yellow Sea (561/565, 98.9%). In contrast, the P and MI of infection were relatively low in the East Sea (n = 239, P = 8.37%, MI = 1.25 larvae/host). A. pegreffii was not found from the East Sea and 52.0% (13/25) of the nematodes were identified as A. simplex. Most of them were found in the body cavity or digestive tract of common squid, which are rarely consumed raw by humans. Considering the differenences in anisakid nematode species distribution and their microhabitat in common squid, it remains unclear whether common squid plays an important role in the epidemiology of human anisakis infection in Korea. Further extensive identification of anisakid nematodes in common squid, with geographical and seasonal information will be necessary.
Recently, a series of lawsuits were filed in Korea claiming tort liability against tobacco companies. The Supreme Court has already issued decisions in some cases, while others are still pending. The primary issue in these cases is whether the epidemiological evidence submitted by the plaintiffs clearly proves the causal relationship between smoking and disease as required by civil law. Proving causation is difficult in tobacco lawsuits because factors other than smoking are involved in the development of a disease, and also because of the lapse of time between smoking and the manifestation of the disease. The Supreme Court (Supreme Court Decision, 2011Da22092, April 10, 2014) has imposed some limitations on using epidemiological evidence to prove causation in tobacco lawsuits filed by smokers and their family members, but these limitations should be reconsidered. First, the Court stated that a disease can be categorized as specific or non-specific, and for each disease type, causation can be proven by different types of evidence. However, the concept of specific diseases is not compatible with multifactor theory, which is generally accepted in the field of public health. Second, when the epidemiological association between the disease and the risk factor is proven to be significant, imposing additional burdens of proof on the plaintiff may considerably limit the plaintiff’s right to recovery, but the Court required the plaintiffs to provide additional information such as health condition and lifestyle. Third, the Supreme Court is not giving greater weight to the evidential value of epidemiological study results because the Court focuses on the fact that these studies were group-level, not individual-level. However, group-level studies could still offer valuable information about individual members of the group, e.g., probability of causation. PMID:27055545
Vanderpump, Mark P
Iodine is an essential component of the thyroid hormones thyroxine (T4) and triiodothyronine (T3) produced by the thyroid gland. Iodine deficiency impairs thyroid hormone production and has adverse effects throughout life, particularly early in life as it impairs cognition and growth. Iodine deficiency remains a significant problem despite major national and international efforts to increase iodine intake, primarily through the voluntary or mandatory iodization of salt. Recent epidemiological data suggest that iodine deficiency is an emerging issue in industrialized countries, previously thought of as iodine-sufficient. International efforts to control iodine deficiency are slowing, and reaching the third of the worldwide population that remains deficient poses major challenges.
A study of epidemiology of respiratory viruses that was begun in the early 1960's is described. Locations selected for the study included a Wisconsin University housing village, a second grade school population, individual volunteers who associated socially, married couples, and the winter-over population at McMurdo Bay and at Scott Base in the Antarctic. It was concluded that most rhinovirus transmission is through aerosolized particles. Air filtration and careful nasal sanitation with virucidal tissues are determined to be effective in blocking rhinovirus transmission and should be useful in both isolated space colonies and in ordinary earth-bound populations.
Fox, G J; Menzies, D
Immunological impairment plays a major role in the epidemiology of TB. Globally, the most common causes of immunological impairment are malnutrition, diabetes, HIV/AIDS, aging, and smoking. With the notable exception of HIV, each factor leads to relatively mild immunological impairment in individuals. However, as these conditions affect a significant proportion of the population, they contribute substantially to the incidence of TB at a global scale. Understanding immunological impairment is central to understanding the global TB pandemic, and vital to the development of effective disease control strategies.
McNeill, Katharine A
Brain tumors are the commonest solid tumor in children, leading to significant cancer-related mortality. Several hereditary syndromes associated with brain tumors are nonfamilial. Ionizing radiation is a well-recognized risk factor for brain tumors. Several industrial exposures have been evaluated for a causal association with brain tumor formation but the results are inconclusive. A casual association between the common mutagens of tobacco, alcohol, or dietary factors has not yet been established. There is no clear evidence that the incidence of brain tumors has changed over time. This article presents the descriptive epidemiology of the commonest brain tumors of children and adults.
Sohn, Chang Hwan; Ryoo, Seung Mok; Lim, Kyoung Soo; Kim, Won; Lim, Hoon; Oh, Bum Jin
Antidotes for toxicological emergencies can be life-saving. However, there is no nationwide estimation of the antidotes stocking amount in Korea. This study tried to estimate the quantities of stocking antidotes at emergency department (ED). An expert panel of clinical toxicologists made a list of 18 emergency antidotes. The quantity was estimated by comparing the antidote utilization frequency in a multicenter epidemiological study and the nation-wide EDs' data of National Emergency Department Information System (NEDIS). In an epidemiological study of 11 nationwide EDs from January 2009 to December 2010, only 92 (1.9%) patients had been administered emergency antidotes except activated charcoal among 4,870 cases of acute adult poisoning patients. Comparing with NEDIS data, about 1,400,000 patients visited the 124 EDs nationwide due to acute poisoning and about 103,348 adult doses of the 18 emergency antidotes may be required considering poisoning severity score. Of these, 13,224 (1.9%) adult doses of emergency antidotes (575 of atropine, 144 of calcium gluconate or other calcium salts, 2,587 of flumazenil, 3,450 of N-acetylcysteine, 5,893 of pralidoxime, 287 of hydroxocobalamin, 144 of sodium nitrite, and 144 of sodium thiosulfate) would be needed for maintaining the present level of initial treatment with emergency antidotes at EDs in Korea.
Lee, Su In; Rayamahji, Nabin; Lee, Won Jung; Cha, Seung Bin; Shin, Min Kyung; Roh, Yu Mi; Yoo, Han Sang
Adherence factors and enterotoxins are major virulence factors of enterotoxigenic Escherichia coli (ETEC). Antibiotics have been used frequently for the treatment and prevention of ETEC infection in piggeries worldwide, including Korea. Therefore, data on both virulence profiles and antibiotic resistance patterns are useful in the epidemiological study of ETEC. A total number of 198 E. coli field isolates were examined. The most prevalent pathotype was F1, followed by a combination of F1 and EAST1. All of the 71 isolates were resistant to more than 2 antibiotics used in a disk diffusion test, and 87.94% of the isolates were found to be resistant to more than 4 antibiotics. Investigations were also conducted to correlate the virulence gene profiles with antibiogram and pulsed-field gel electrophoresis (PFGE). Although a high degree of polymorphism was noted among strains having the same virulence patterns, the highest similarity pattern was observed carrying the same virulence profiles and similar antibiogram. Thus, investigation of both virulence profiles and antibiogram is essential to the epidemiological study of ETEC. Moreover, the PFGE method might be applicable as a tool to reveal genetic relatedness among E. coli strains from piggeries in Korea.
Kwon, Insook; Lee, Dong-Ok; Kim, Elli; Kim, Hyun-Young
This research is about sexual violence among men in the military in South Korea. The authors investigated the frequencies, causes, and circumstances surrounding sexual violence and looked for characteristic features of sexual violence among men in the military in South Korea. They found a high frequency of physical sexual violence and a high level…
... COMMISSION Polyethylene Terephthalate (PET) Film From Korea Determination On the basis of the record \\1... antidumping duty order on polyethylene terephthalate (PET) film from Korea would not be likely to lead to... contained in USITC Publication 4254 (August 2011), entitled Polyethylene Terephthalate (PET) Film from...
Korea opened up to foreign intercourse in 1876, when the country concluded its first international treaty with Japan. Similar treaties with European and American nations followed during the 1880s. The period until 1910, when Korea was annexed to the Japanese Empire, saw manifold attempts to reform as well as resistance to these reforms. Against…
In Korea, e-learning is becoming increasingly prevalent and spreading into various aspects of human resources development. Korea's Ministry of Education and Human Resources Development (MOEHRD) and Ministry of Labor (MOL) have been especially active in establishing the legal basis and institutional framework to make e-learning a reality.…
Examines the impact of Japanese nationalistic thought on the administrative systems and structures of colonial and modern higher education in Korea and analyzes Japanese educational policy in Korea in the colonial period (1910-1945). Identifies beneficial and negative impacts of the Japanese colonial education system. (SLD)
Choi, Dong Geun; de Vries, Henk J.
The Republic of Korea is a forerunner in integrating the topic of standardization into engineering education at the academic level. This study investigates developments and evolutions in the planning and operating of the University Education Promotion on Standardization (UEPS) in Korea. This paper examines why the Korean government initiated the…
Lee, Seung-yeon; Hong, Jun Sung; Espelage, Dorothy L.
This article reviews risk factors for youth suicide in South Korea (hereafter referred to as Korea), based on the ecological systems theory. Although youth suicide is a major concern for Korean society, understanding of this phenomenon has been limited since most of the empirical studies address personal characteristics without much consideration…
Song, Jae Jung
This monograph discusses South Korea's language situation in a language policy and planning context. This monograph consists of four parts. Part 1 presents a genetic, typological and sociolinguistic description of South Korea's national language, and an overview of minority languages, including English as well as other languages, recently…
This research is a qualitative case study of native English instructors at the Gyeonggi-do Institute for Foreign Language Education (GIFLE) in South Korea. A literature review of issues regarding expatriate educators is included. The guiding questions for this study include why these instructors chose to become educators, move to South Korea, and…
The spread of the English language is a global phenomenon, but it has a particular resonance in South Korea, where English is second only to Korean as a common language. The paper examines the current educational context in South Korea and the policy and practice issues that arise within this context regarding teacher education in English as a…
Lee, Romee; Heo, Gyeong Mi; Kim, Jinhee
The importance of professional workers' multicultural competence (MC) is increasingly noted in Korea, which is shifting into a multicultural society. This study investigates the current location of the discussion regarding the MC of professional workers in Korea using reviews of existing studies in international and Korean contexts. This paper…
9 O PPO RTUN ITIES...will stress South Korea’s ability to absorb them into their society and economy over the long-run. ECONOMIC INSTABILITY The North Korean economy is in...enormous costs of absorbing the broken economy of the North.40 When contrasted with German reunification, the economy and infrastructure of North Korea are
Early childhood education has always been considered important in Korea, with the education of the child valued highly, regardless of the parent's educational background or socioeconomic status. The main social facility for early childhood education outside home in Korea is called "Yoo Chee Won," which means kindergarten. This paper…
Kim, Jin Il; Lee, Ilseob; Park, Sehee; Lee, Sangmoo; Hwang, Min-Woong; Bae, Joon-Yong; Heo, Jun; Kim, Donghwan; Jang, Seok-Il; Kim, Kabsu; Park, Man-Seong
Influenza A virus (IAV) can infect avian and mammalian species, including humans. The genome nature of IAVs may contribute to viral adaptation in different animal hosts, resulting in gene reassortment and the reproduction of variants with optimal fitness. As seen again in the 2009 swine-origin influenza A H1N1 pandemic, pigs are known to be susceptible to swine, avian, and human IAVs and can serve as a 'mixing vessel' for the generation of novel IAV variants. To this end, the emergence of swine influenza viruses must be kept under close surveillance. Herein, we report the isolation and phylogenetic study of a swine IAV, A/swine/Korea/PL01/2012 (swPL01, H3N2 subtype). After screening nasopharyngeal samples from pigs in the Gyeongsangnam-do region of Korea from December 2011 to May 2012, we isolated the swPL01 virus and sequenced its all of 8 genome segments (polymerase basic 2, PB2; polymerase basic 1, PB1; polymerase acidic, PA; hemagglutinin, HA; nucleocapsid protein, NP; neuraminidase, NA; matrix protein, M; and nonstructural protein, NS). The phylogenetic study, analyzed with reference strains registered in the National Center for Biotechnology Information (NCBI) database, indicated that the swPL01 virus was similar to the North American triple-reassortant swine strains and that the HA gene of the swPL01 virus was categorized into swine H3 cluster IV. The swPL01 virus had the M gene of the triple-reassortant swine H3N2 viruses, whereas that of other contemporary strains in Korea was transferred from the 2009 pandemic H1N1 virus. These data suggest the possibility that various swine H3N2 viruses may co-circulate in Korea, which underlines the importance of a sustained surveillance system against swine IAVs.
Seoul, Korea, is in the throes of change--in the way its people live, in the jobs they do, and in the makeup of its populace. The city of Seoul proper houses 1 out of every 4 Koreans. Home to 95 of Korea's 100 largest trading companies and 42 of the 46 family-based industrial conglomerates--Seoul controls Korean commerce. Employment opportunities have kept pace with Seoul's rapidly growing labor supply resulting in low unemployment by developing country standards. Only 12.3% of Koreans now live below the poverty line, down from nearly 41% in 1962. The real per capita income in Seoul rose from a dismal $87 in 1962 to nearly $2000 in 1985. The completion of 2 commuter rail lines in 1974 accelerated the movement of people out of the city and into suburban areas, concentrating urban growth along the railway corridors. Population densities in the city's central wards make Seoul 1 of the world's most densely populated cities. Although Seoul's population is young--27.9% of the population was under age 15 in 1983-- it is becoming increasingly dominated by those of working age. Seoul is essentially a city of migrants; more than 1/2 of the city's grwoth since 1960 is attributable to in-migration. Although the trend is toward rising white-collar employment, Seoul is still a blue-collar town. Seoul's educational system is so highly regarded in Korea that families move to seoul just to enroll their children. Korean spending patterns are influenced greatly by the Korean penchant for higher education.
Population aging in Korea is projected to be the most rapid among Organisation for Economic Co-operation and Development (OECD) countries between 2000 and 2050. However, social spending in Korea remains low, reflecting Korea's relatively young population, limited health and long-term care insurance coverage, and immaturity of its pension system. As these factors evolve in coming years, social spending in Korea is likely to rise toward the OECD average. Sustaining economic growth requires policies to mitigate the impact of rapid population aging by providing social protection for the elderly population. Korea confronts difficult challenges in balancing economic growth and social protection for the elderly population, whereas also ensuring efficiency in social spending.
Mann, Nancy K
This historical narrative highlights the origin and development of the dental hygiene profession in South Korea. The legacy of early American missionaries to Korea includes profound and long-lasting contributions in medicine, education and theology. Many of Korea's top universities today have their roots in the missionary schools of the late nineteenth century, including Yonsei University, home of the first dental hygiene program in Korea. From Yonsei in Seoul, the dental hygiene profession spread throughout the country, includingtheAmerican missionary-based program in Kwangju in 1977. Contributions included clinical and didactic education, as well as professional leadership and development. American dental missionaries developed the profession of dental hygiene in Korea, and provided guidance to Korean dentists and hygienists for its growth and expansion.
Podenas, Sigitas; Byun, Hye-Woo; Kim, Sam-Kyu
Korean species of the crane fly genus Rhipidia Meigen, 1818 (Diptera: Limoniidae), are taxonomically revised. Rhipidia (Rhipidia) serena, new species, is described and figured. Rhipidia (R.) longa Zhang, Li, Yang, 2014, R. (R.) maculata Meigen, 1818 and R. (R.) sejuga Zhang, Li, Yang, 2014 are recorded for the first time in Korea. Previously known species, Rhipidia (R.) septentrionis Alexander, 1913 is redescribed and illustrated. Identification key for all Korean Rhipidia species is given. Most antennae, wings, male and female terminalia of all species are illustrated for the first time.
27. Recreation/Education Services6-Satisfaction Score Analisis 121 29. Women-in Co--mba Attitude Sore Anaysis 123 28. then i Comy Atitude ,Scii Anaysis... data with respect to some known aspects of soldiering in Korea ard women in the Army;.,and (2) to explore for some newunderstanding of the problem areas...dbsents and suggetiohs: The write-in data is not the focus of this report. That information was reviewed, summarized and presented, to the comma nd-for
2007. 46 See http://www.state.gov/s/ct/rls/crt/2006/82736.htm at p. 147. 47 Yi Sang-il and Chin Se-ku. Yongbyon nuclear facility can be disabled within...Choe Sang- hun and David E. Sanger, North Korea claims U.S. will remove sanctions, International Herald Tribune, September 4, 2007, p. 5. 52 Japanese...several North Korean attempts in late 2006 through the spring of 2007 to smuggle conventional arms, including machine guns , automatic rifles, and anti
Cha, Yoon Ki; Kim, Yookyung; Kim, Yoon Kyung
Asbestosis is the most important change noted in the lung parenchyma after environmental and occupational exposure to asbestos fibers. It is characterized by diffuse interstitial pulmonary fibrosis. In Korea, the incidence of asbestosis will continue to increase for many years to come and the government enacted the Asbestos Damage Relief Law in 2011 to provide compensation to those suffering from asbestos-related diseases. Radiologic evaluation is necessary for diagnosis of asbestosis, and radiologists play a key role in this process. Therefore, it is important for radiologists to be aware of the various imaging features of asbestosis. PMID:27587956
Lee, Y.; Choi, K.; Kim, Y.; Ahn, Y.; Chang, M.
In Korea currently 4 research ships are under operating in Korea, after the first research vessel equipped shipborne gravity meter was introduced in 1990s. These are Onnuri(launch 1991) of KORDI(Korea Ocean Research & Development Institute), Haeyang2000(launch 1996), Badaro1(launch 2002) of NORI(National Oceanographic Research Institute) and Tamhae2(launch 1997) of KIGAM(Korea Institute of Geoscience and Mineral Resources). Those of research vessel, Haeyang2000 have observed marine gravity data over 150,000 points each year from year 1996 to year 2003. Haeyang2000, about 2,500 tons, is unable to operate onshore so NORI has constructed another 600 tons research ship Badaro1 that has observed marine gravity data onshore since year 2002. Haeyang2000 finished observing marine gravity data offshore within Korean territorial waters until year 2003. Currently Badaro1 is observing marine gravity data onshore. These shipborne gravity data will be very useful and important on geodesy and geophysics research also those data can make a contribution to developing these studies. In this study NORI's shipbrne gravity data from 1996 to 2007 has been processed for fundamental data to compute Korean precise geoid. Marine gravity processing steps as followed. 1. Check the time sequence, latitude and longitude position, etc. of shipborne gravity data 2. Arrangement of the tide level below the pier and meter drift correction of each cruise. 3. Elimination of turning points. 4. The time lag correction. 5. Computation of RV's velocities, Heading angles and the Eötvös correction. 6. Kalman filtering of GPS navigation data using cross-over points. 7. Cross-over correction using least square adjustment. About 2,058,000 points have been processed with NORI's marine gravity data from 1996 to 2007 in this study. The distribution of free-air anomalies was -41.0 mgal to 136.0 mgal(mean 8.90mgal) within Korean territorial waters. The free-air anomalies processed with the marine gravity data are
Chakrabarti, Arunaloke; Bonifaz, Alexandro; Gutierrez-Galhardo, Maria Clara; Mochizuki, Takashi; Li, Shanshan
Sporotrichosis is an endemic mycosis caused by the dimorphic fungus Sporothrix schenckii sensu lato. It has gained importance in recent years due to its worldwide prevalence, recognition of multiple cryptic species within the originally described species, and its distinctive ecology, distribution, and epidemiology across the globe. In this review, we describe the current knowledge of the taxonomy, ecology, prevalence, molecular epidemiology, and outbreaks due to S. schenckii sensu lato. Despite its omnipresence in the environment, this fungus has remarkably diverse modes of infection and distribution patterns across the world. We have delved into the nuances of how sporotrichosis is intimately linked to different forms of human activities, habitats, lifestyles, and environmental and zoonotic interactions. The purpose of this review is to stimulate discussion about the peculiarities of this unique fungal pathogen and increase the awareness of clinicians and microbiologists, especially in regions of high endemicity, to its emergence and evolving presentations and to kindle further research into understanding the unorthodox mechanisms by which this fungus afflicts different human populations.
Dodds, Richard Matthew; Roberts, Helen Clare; Cooper, Cyrus; Sayer, Avan Aihie
The aim of this review is to describe the epidemiology of sarcopenia, specifically prevalence, health outcomes, and factors across the life course that have been linked to its development. Sarcopenia definitions involve a range of measures (muscle mass, strength, and physical performance), which tend to decline with age, and hence sarcopenia becomes increasingly prevalent with age. Less is known about prevalence in older people in hospital and care homes, although it is likely to be higher than in community settings. The range of measures used, and the cutpoints suggested for each, presents a challenge for comparing prevalence estimates between studies. The importance of sarcopenia is highlighted by the range of adverse health outcomes that strength and physical performance (and to a lesser extent, muscle mass) have been linked to. This is shown most strikingly by the finding of increased all-cause mortality rates among those with weaker grip strength and slower gait speed. A life course approach broadens the window for our understanding of the etiology of sarcopenia and hence the potential intervention. An example is physical activity, with increased levels across midadulthood appearing to increase muscle mass and strength in early old age. Epidemiologic studies will continue to make an important contribution to our understanding of sarcopenia and possible avenues for intervention and prevention.
Khoury, Muin J
We live in the era of genomics and big data. Evaluating the impact on health of large-scale biological, social, and environmental data is an emerging challenge in the field of epidemiology. In the past 3 years, major discussions and plans for the future of epidemiology, including with several recommendations for actions to transform the field, have been launched by 2 institutes within the National Institutes of Health. In the present commentary, I briefly explore the themes of these recommendations and their effects on leadership, resources, cohort infrastructure, and training. Ongoing engagement within the epidemiology community is needed to determine how to shape the evolution of the field and what truly matters for changing population health. We also need to assess how to leverage existing epidemiology resources and develop new studies to improve human health. Readers are invited to examine these recommendations, consider others that might be important, and join in the conversation about the future of epidemiology.
Kim, H J; Ahn, Y S; Lee, S G
The purpose of this study is to compare the difference in health status between South Koreans and North Koreans and to identify factors responsible for the remarkable improvements in the health status of South Koreans. In order to examine the causes of the difference in health level, the health indices and their determinants of two Koreas were analyzed in time order. As of the year 2000, the average life expectancy at birth is 71.0 years for men and 78.6 years for women in South Korea, which is longer than that of North Korea by 8.1 for men and 11.2 for women. Infant mortality rate in 1998 was 9.0 per 1,000 live births in South Korea and 54.0 in North Korea. Since being liberated from Japanese ruling in 1945, South Korea has achieved remarkable economic growth under democracy and a market economy system. On the other hand, North Korea has maintained a socialistic system. North Korea has suffered from economic crisis since the 1990s. From this point it could be said that economic status is the major factor for the differences in health level between the two Koreas. Economic status not only directly influences health level but also indirectly affects it through influences on nutrition, hygiene, health resources, and other intervening factors. The South Korean government has concentrated its limited resources on public health activities such as tuberculosis control, family planning (FP), and maternal and child health (MCH) programmes whereas the private sector has taken charge of constructing the health delivery system including health facilities and human resources. In order to solve the problem, which might occur in the private-oriented medical care system, the South Korean government has introduced the national health insurance programme and enforced regulation policies. Many developing countries which are suffering from poverty and disease, can learn from the experience of Korea that had suffered from similar problems up to the early 1970s.
Hasan, Nur A.; Cebula, Thomas A.; Colwell, Rita R.; Robison, Richard A.; Johnson, W. Evan; Crandall, Keith A.
The post-genomic era is characterized by the direct acquisition and analysis of genomic data with many applications, including the enhancement of the understanding of microbial epidemiology and pathology. However, there are a number of molecular approaches to survey pathogen diversity, and the impact of these different approaches on parameter estimation and inference are not entirely clear. We sequenced whole genomes of bacterial pathogens, Burkholderia pseudomallei, Yersinia pestis, and Brucella spp. (60 new genomes), and combined them with 55 genomes from GenBank to address how different molecular survey approaches (whole genomes, SNPs, and MLST) impact downstream inferences on molecular evolutionary parameters, evolutionary relationships, and trait character associations. We selected isolates for sequencing to represent temporal, geographic origin, and host range variability. We found that substitution rate estimates vary widely among approaches, and that SNP and genomic datasets yielded different but strongly supported phylogenies. MLST yielded poorly supported phylogenies, especially in our low diversity dataset, i.e., Y. pestis. Trait associations showed that B. pseudomallei and Y. pestis phylogenies are significantly associated with geography, irrespective of the molecular survey approach used, while Brucella spp. phylogeny appears to be strongly associated with geography and host origin. We contrast inferences made among monomorphic (clonal) and non-monomorphic bacteria, and between intra- and inter-specific datasets. We also discuss our results in light of underlying assumptions of different approaches. PMID:25737810
Moon, Eun-Kyeong; Park, Hyeon Jin; Oh, Chang-Mo; Jung, Kyu-Won; Shin, Hee Young; Park, Byung Kiu; Won, Young-Joo
Background In Korea, cancer is the third leading cause of death among adolescents and young adults (AYAs). However, cancer incidence and survival trends among AYAs (15–29 years) have never been studied in Korea. Therefore, this study aimed to investigate the incidence and relative survival rates and their trends among AYAs in Korea. Materials and Methods Cancer incidence data from 1999–2010 were obtained from the Korea Central Cancer Registry (KCCR). Each cancer was classified into subgroups according to the National Cancer Institute Surveillance, Epidemiology, and End Results (SEER) AYA site recode. Percent distributions, age-specific incidence rates, age-standardized incidence rates per million, and annual percent changes (APCs) were calculated for AYAs according to sex. Five-year relative survival rates were estimated for cases diagnosed between 1993 and 2010 and followed up to 2011. Results The age-standardized incidence rates of all cancers combined were 196.4 and 367.8 per million for males and females, respectively (male-to-female (M/F) ratio: 0.5). The age-standardized incidence rates increased from 208.7 per million in 1999 to 396.4 per million in 2010, and the APC was 6.3% (P<0.001). The five most common cancers among AYAs were thyroid carcinoma, non-Hodgkin lymphoma, stomach carcinoma, breast carcinoma, and acute myeloid leukemia. In males, the 5-year relative survival rate improved, from 46.5% in 1993–1995 to 75.9% in 2006–2010. In females, the 5-year relative survival rate also improved, from 66.7% in 1993–1995 to 89.1% in 2006–2010. Conclusions Our study showed increases in cancer incidence and improvements in the 5-year relative survival rate among Korean AYAs. This study also provides additional data regarding temporal and geographic trends in cancer that may enhance future efforts to identify factors affecting cancer incidence and responses to treatment among AYAs. PMID:24789075
Genetic epidemiologic studies indicate that all ten personality disorders (PDs) classified on the DSM-IV axis II are modestly to moderately heritable. Shared environmental and nonadditive genetic factors are of minor or no importance. No sex differences have been identified. Multivariate studies suggest that the extensive comorbidity between the PDs can be explained by three common genetic and environmental risk factors. The genetic factors do not reflect the DSM-IV cluster structure, but rather: i) broad vulnerability to PD pathology or negative emotionality; ii) high impulsivity/low agreeableness; and iii) introversion. Common genetic and environmental liability factors contribute to comorbidity between pairs or clusters of axis I and axis II disorders. Molecular genetic studies of PDs, mostly candidate gene association studies, indicate that genes linked to neurotransmitter pathways, especially in the serotonergic and dopaminergic systems, are involved. Future studies, using newer methods like genome-wide association, might take advantage of the use of endophenotypes. PMID:20373672
Genetic epidemiologic studies indicate that all ten personality disorders (PDs) classified on the DSM-IV axis II are modestly to moderately heritable. Shared environmental and nonadditive genetic factors are of minor or no importance. No sex differences have been identified, Multivariate studies suggest that the extensive comorbidity between the PDs can be explained by three common genetic and environmental risk factors. The genetic factors do not reflect the DSM-IV cluster structure, but rather: i) broad vulnerability to PD pathology or negative emotionality; ii) high impulsivity/low agreeableness; and iii) introversion. Common genetic and environmental liability factors contribute to comorbidity between pairs or clusters of axis I and axis II disorders. Molecular genetic studies of PDs, mostly candidate gene association studies, indicate that genes linked to neurotransmitter pathways, especially in the serotonergic and dopaminergic systems, are involved. Future studies, using newer methods like genome-wide association, might take advantage of the use of endophenotypes.
Svensson, Kerstin; Bäck, Erik; Eliasson, Henrik; Berglund, Lennart; Granberg, Malin; Karlsson, Linda; Larsson, Pär; Forsman, Mats
Summer outbreaks of tularemia that occurred from 1995 through 2005 in 2 locations in Sweden affected 441 persons. We performed an epidemiologic investigation of these outbreaks using a novel strategy, involving high-resolution genotyping of Francisella tularensis isolates obtained from 136 patients (using 18 genetic markers developed from 6 F. tularensis genome sequences) and interviews with the patients. Strong spatial associations were found between F. tularensis subpopulations and the places of disease transmission; infection by some subpopulations occurred within areas as small as 2 km2, indicating unidentified environmental point sources of tularemia. In both locations, disease clusters were associated with recreational areas beside water, and genetic subpopulations were present throughout the tularemia season and persisted over years. High-resolution genotyping in combination with patients’ statements about geographic places of disease transmission provided valuable indications of likely sources of infection and the causal genotypes during these tularemia outbreaks. PMID:19961673
The Department of Energy (DOE) and its predecessor agencies have a long history of epidemiologic research programs. The main focus of these programs has been the Health and Mortality Study of the DOE work force. This epidemiologic study began in 1964 with a feasibility study of workers at the Hanford facility. Studies of other populations exposed to radiation have also been supported, including the classic epidemiologic study of radium dial painters and studies of atomic bomb survivors. From a scientific perspective, these epidemiologic research program have been productive, highly credible, and formed the bases for many radiological protection standards. Recently, there has been concern that, although research results were available, the data on which these results were based were not easily obtained by interested investigators outside DOE. Therefore, as part of an effort to integrate and broaden access to its epidemiologic information, the DOE has developed the Comprehensive Epidemiologic Data Resource (CEDR) Program. Included in this effort is the development of a computer information system for accessing the collection of CEDR data and its related descriptive information. The epidemiologic data currently available through the CEDAR Program consist of analytic data sets, working data sets, and their associated documentation files. In general, data sets are the result of epidemiologic studies that have been conducted on various groups of workers at different DOE facilities during the past 30 years.
Risser, Jan M H; Risser, William L; Risser, Amanda L
This article describes the epidemiologic profiles of sexually transmitted infections seen in US women. We present a brief description of the infectious agent, describe the epidemiology of the infection among women in terms of race/ethnicity and age (if those data are available), and present what is known about the behavioral risk factors associated with acquisition.
Morton, N E
Starting from a broad definition of genetic epidemiology, current developments in association, segregation, and linkage analysis of complex inheritance are considered together with integration of genetic and physical maps and resolution of genetic heterogeneity. Mitochondrial inheritance, imprinting, uniparental disomy, pregressive amplification, and gonadal mosaicism are some of the novel mechanisms discussed, with speculation about the future of genetic epidemiology.
Shoag, Jonathan; Tasian, Greg E; Goldfarb, David S; Eisner, Brian H
Historically nephrolithiasis was considered a disease of dehydration and abnormal urine composition. However, over the past several decades, much has been learned about the epidemiology of this disease and its relation to patient demographic characteristics and common systemic diseases. Here we review the latest epidemiologic studies in the field.
Han, Cliff; Sikorski, Johannes; Lapidus, Alla; Nolan, Matt; Glavina Del Rio, Tijana; Tice, Hope; Cheng, Jan-Fang; Lucas, Susan; Chen, Feng; Copeland, Alex; Ivanova, Natalia; Mavromatis, Konstantinos; Ovchinnikova, Galina; Pati, Amrita; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D; Chain, Patrick; Saunders, Elizabeth; Brettin, Thomas; Göker, Markus; Tindall, Brian J; Bristow, Jim; Eisen, Jonathan A; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Detter, John C
Kangiella koreensis (Yoon et al. 2004) is the type species of the genus and is of phylogenetic interest because of the very isolated location of the genus Kangiella in the gammaproteobacterial order Oceanospirillales. K. koreensis SW-125(T) is a Gram-negative, non-motile, non-spore-forming bacterium isolated from tidal flat sediments at Daepo Beach, Yellow Sea, Korea. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first completed genome sequence from the genus Kangiella and only the fourth genome from the order Oceanospirillales. This 2,852,073 bp long single replicon genome with its 2647 protein-coding and 48 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
Lee, Jong-Keuk; Hong, Young Mi; Jang, Gi Young; Yun, Sin Weon; Yu, Jeong Jin; Yoon, Kyung Lim; Lee, Kyung-Yil; Kil, Hong-Rang
In order to perform large-scale genetic studies of Kawasaki disease (KD) in Korea, the Korean Kawasaki Disease Genetics Consortium (KKDGC) was formed in 2008 with 10 hospitals. Since the establishment of KKDGC, there has been a collection of clinical data from a total of 1198 patients, and approximately 5 mL of blood samples per patient (for genomic deoxyribonucleic acid and plasma isolation), using a standard clinical data collection form and a nation-wide networking system for blood sample pick-up. In the clinical risk factor analysis using the collected clinical data of 478 KD patients, it was found that incomplete KD type, intravenous immunoglobulin (IVIG) non-responsiveness, and long febrile days are major risk factors for coronary artery lesions development, whereas low serum albumin concentration is an independent risk factor for IVIG non-responsiveness. In addition, we identified a KD susceptibility locus at 1p31, a coronary artery aneurysm locus (KCNN2 gene), and the causal variant in the C-reactive protein (CRP) promoter region, as determining the increased CRP levels in KD patients, by means of genome-wide association studies. Currently, this consortium is continually collecting more clinical data and genomic samples to identify the clinical and genetic risk factors via a single nucleotide polymorphism chip and exome sequencing, as well as collaborating with several international KD genetics teams. The consortium-based approach for genetic studies of KD in Korea will be a very effective way to understand the unknown etiology and causal mechanism of KD, which may be affected by multiple genes and environmental factors.