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Sample records for korea epidemiological genomic

  1. Molecular epidemiology of norovirus in South Korea.

    PubMed

    Lee, Sung-Geun; Cho, Han-Gil; Paik, Soon-Young

    2015-02-01

    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.

  2. Molecular epidemiology of norovirus in South Korea.

    PubMed

    Lee, Sung-Geun; Cho, Han-Gil; Paik, Soon-Young

    2015-02-01

    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. PMID:25441425

  3. Molecular epidemiology of norovirus in South Korea

    PubMed Central

    Lee, Sung-Geun; Cho, Han-Gil; Paik, Soon-Young

    2015-01-01

    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. [BMB Reports 2015; 48(2): 61-67] PMID:25441425

  4. Epidemiology & Genomics Research Program

    Cancer.gov

    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.

  5. Epidemiology of Postherpetic Neuralgia in Korea

    PubMed Central

    Hong, Myong-Joo; Kim, Yeon-Dong; Cheong, Yong-Kwan; Park, Seon-Jeong; Choi, Seung-Won; Hong, Hyon-Joo

    2016-01-01

    Abstract Postherpetic neuralgia (PHN) is a disease entity defined as persistent pain after the acute pain of herpes zoster gradually resolves. It is associated with impaired daily activities, resulting in reduced quality of life. General epidemiological data on PHN is necessary for the effective management. However, data on the epidemiology of PHN in Korea is lacking. The aim of this study was to evaluate the epidemiological features of PHN in the general population. We used population-based medical data for 51,448,491 subscribers to the Health Insurance Service in the year of 2013 to analyze of PHN epidemiology in Korea, such as the incidence, regional distribution, seasonal variation, and healthcare resource utilization. Total number of patients and medical cost on PHN were analyzed from 2009 to 2013. Findings indicate that the incidence of PHN in Korea was 2.5 per 1000 person-years, which was strongly correlated with age and sex. There were no differences in seasonal variation or regional distribution. The medical cost increased steadily over the study period. When admitted to general hospitals, patients with PHN were mainly managed in the dermatology and anesthesiology departments. The incidence and prevalence rates of PHN in Koreans appear to be considerably higher compared to those in western populations, while the sex and age predisposition was similar. Considering that the pain associated with PHN can have a marked impact on a patient's quality of life resulting in a medicosocial economic burden, anesthesiology physicians have an important role in primary care in Korea. Future research on the cost-effectiveness of the management of PHN is needed. PMID:27057902

  6. Genomic Resources for Cancer Epidemiology

    Cancer.gov

    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.

  7. A nationwide epidemiological study of testicular torsion in Korea.

    PubMed

    Lee, Sol Min; Huh, Jung-Sik; Baek, Minki; Yoo, Koo Han; Min, Gyeong Eun; Lee, Hyung-Lae; Lee, Dong-Gi

    2014-12-01

    Testicular torsion is a surgical emergency in the field of urology. Knowledge of the epidemiology and pathophysiology is significant to an urologist. However, the epidemiology of testicular torsion in Korea has not been studied. We performed a nationwide epidemiological study to improve knowledge of the epidemiology of testicular torsion. From 2006-2011, the Korean Urologic Association began the patient registry service. The annual number of patients with testicular torsion from 2006 to 2011 were 225, 250, 271, 277, 345, and 210, respectively. The overall incidence of testicular torsion in males was 1.1 per 100,000; However, the incidence in men less than 25 yr old was 2.9 per 100,000. Adolescents showed the highest incidence. Total testicular salvage rate was 75.7% in this survey. There was no geographic difference of testicular salvage rate. Minimizing the possibility of orchiectomy for testicular torsion is important to improve public awareness to expedite presentation and provider education to improve diagnosis and surgery. PMID:25469070

  8. A nationwide epidemiological study of testicular torsion in Korea.

    PubMed

    Lee, Sol Min; Huh, Jung-Sik; Baek, Minki; Yoo, Koo Han; Min, Gyeong Eun; Lee, Hyung-Lae; Lee, Dong-Gi

    2014-12-01

    Testicular torsion is a surgical emergency in the field of urology. Knowledge of the epidemiology and pathophysiology is significant to an urologist. However, the epidemiology of testicular torsion in Korea has not been studied. We performed a nationwide epidemiological study to improve knowledge of the epidemiology of testicular torsion. From 2006-2011, the Korean Urologic Association began the patient registry service. The annual number of patients with testicular torsion from 2006 to 2011 were 225, 250, 271, 277, 345, and 210, respectively. The overall incidence of testicular torsion in males was 1.1 per 100,000; However, the incidence in men less than 25 yr old was 2.9 per 100,000. Adolescents showed the highest incidence. Total testicular salvage rate was 75.7% in this survey. There was no geographic difference of testicular salvage rate. Minimizing the possibility of orchiectomy for testicular torsion is important to improve public awareness to expedite presentation and provider education to improve diagnosis and surgery.

  9. Molecular Epidemiology of Human Norovirus in Korea in 2013

    PubMed Central

    Kim, Jae-Seok; Kim, Hyun Soo; Hyun, Jungwon; Kim, Han-Sung; Song, Wonkeun

    2015-01-01

    Norovirus is a major cause of acute gastroenteritis. The molecular epidemiology of norovirus exhibits temporal and geographical fluctuations, and new variants of the GII.4 genotype emerge every 2-3 years to cause global epidemics of acute gastroenteritis. We investigated GI and GII genotypes of human norovirus strains isolated from patients with acute gastroenteritis in Korea in 2013. Norovirus antigen test was performed on 2,980 fecal specimens from January to December 2013. RNA was extracted from norovirus antigen-positive fecal suspensions, and the norovirus capsid (VP1) and polymerase (RdRp) genes were characterized by RT-PCR and sequencing. Of the 230 genotyped strains, GII.4 (77.3%) was the most frequently observed capsid genotype, followed by GII.3 (6.1%) and GII.13 (3.9%). A norovirus GII.4 variant, GII.Pe/GII.4 Sydney 2012, was the most frequently found polymerase/capsid genotype (65.7%), followed by GII.P17/GII.17 (2.1%) and GII.P21/GII.3 (2.1%). Phylogenetic, similarity, and capsid epitope analyses of GII.Pe/GII.4 Sydney 2012 strains were performed. We concluded that the norovirus GII.4 variant, GII.Pe/GII.4 Sydney 2012, was the main cause of norovirus-related gastroenteritis in Korea in 2013. PMID:26421289

  10. Comparative epidemiological features of Japanese encephalitis in the Republic of Korea, China (Taiwan) and Japan

    PubMed Central

    Kono, Reisaku; Kim, Kyong Ho

    1969-01-01

    The epidemiology of Japanese encephalitis in the Republic of Korea from 1949 to 1966 is described and comparisons are made with the situations in Japan and China (Taiwan). Some similarities and some differences are noted. Recent epidemics in Korea coincided with those in southern Japan but the annual fluctuations were more distinct in Korea. The disease mainly affected children in Korea and, in contrast to the situation in Japan, persons in the older age-groups were rarely affected. The authors also discuss the geographical pathology of Japanese encephalitis in Korea. PMID:4308334

  11. [From molecular to genomic and metagenomic epidemiology].

    PubMed

    Zhebrun, A B

    2014-01-01

    The notion "molecular epidemiology" was introduced into scientific literature by Kilburn E. et al. in 1973. The first period of development of infectious diseases molecular epidemiology may be called "genotypic" (1980-1990s). During this period methodology of molecular marking of pathogens for purposes of monitoring of their spread and outbreak detection (novel nomenclature of diphtheria corynebacteria based on ribotyping; international network PulseNet for monitoring food source infections; international database of tuberculosis mycobacteria spoligotypes) was created. The second--"genomic" period started in the 2000s. Molecular epidemiology rapidly went through single markers (genotypes or single genes) to deciphering the whole genome of pathoge "mobileome", "resistome", "virulome" etc. took an important place in the studies of emerging and pandemic infections. Knowledge on genetic mechanisms leading to emergence and global dissemination of novel pathogens give molecular epidemiology its own scientific content and transforms it from a methodical approach to an independent field of epidemiology. The third--"metagenomic" period starts nowadays based on meta-genomic approach that allows to determine the whole set ofgenomes in the studied sample without the cultivation procedure. In the short-term this would lead to a change of a century-long paradigm of diagnostics and control of infections: instead of search of separate (key) pathogens--characteristics of the full specter of microorganisms in the material from patients and environmental samples with its identification up to any taxonomic depth. In the systems of regional and global epidemiologic control a universal monitoring of all known and re-emerging pathogens with construction and maintenance of metagenomic passports of human habitats will be realized. PMID:25286516

  12. [From molecular to genomic and metagenomic epidemiology].

    PubMed

    Zhebrun, A B

    2014-01-01

    The notion "molecular epidemiology" was introduced into scientific literature by Kilburn E. et al. in 1973. The first period of development of infectious diseases molecular epidemiology may be called "genotypic" (1980-1990s). During this period methodology of molecular marking of pathogens for purposes of monitoring of their spread and outbreak detection (novel nomenclature of diphtheria corynebacteria based on ribotyping; international network PulseNet for monitoring food source infections; international database of tuberculosis mycobacteria spoligotypes) was created. The second--"genomic" period started in the 2000s. Molecular epidemiology rapidly went through single markers (genotypes or single genes) to deciphering the whole genome of pathoge "mobileome", "resistome", "virulome" etc. took an important place in the studies of emerging and pandemic infections. Knowledge on genetic mechanisms leading to emergence and global dissemination of novel pathogens give molecular epidemiology its own scientific content and transforms it from a methodical approach to an independent field of epidemiology. The third--"metagenomic" period starts nowadays based on meta-genomic approach that allows to determine the whole set ofgenomes in the studied sample without the cultivation procedure. In the short-term this would lead to a change of a century-long paradigm of diagnostics and control of infections: instead of search of separate (key) pathogens--characteristics of the full specter of microorganisms in the material from patients and environmental samples with its identification up to any taxonomic depth. In the systems of regional and global epidemiologic control a universal monitoring of all known and re-emerging pathogens with construction and maintenance of metagenomic passports of human habitats will be realized.

  13. Genetic Diversity and Reassortment of Hantaan Virus Tripartite RNA Genomes in Nature, the Republic of Korea

    PubMed Central

    Kim, Jeong-Ah; Kim, Won-keun; No, Jin Sun; Lee, Seung-Ho; Lee, Sook-Young; Kim, Ji Hye; Kho, Jeong Hoon; Lee, Daesang; Song, Dong Hyun; Gu, Se Hun; Jeong, Seong Tae; Park, Man-Seong; Kim, Heung-Chul; Klein, Terry A.; Song, Jin-Won

    2016-01-01

    Background Hantaan virus (HTNV), a negative sense tripartite RNA virus of the Family Bunyaviridae, is the most prevalent hantavirus in the Republic of Korea (ROK). It is the causative agent of Hemorrhagic Fever with Renal Syndrome (HFRS) in humans and maintained in the striped field mouse, Apodemus agrarius, the primary zoonotic host. Clinical HFRS cases have been reported commonly in HFRS-endemic areas of Gyeonggi province. Recently, the death of a member of the ROK military from Gangwon province due to HFRS prompted an investigation of the epidemiology and distribution of hantaviruses in Gangwon and Gyeonggi provinces that border the demilitarized zone separating North and South Korea. Methodology and Principal Findings To elucidate the geographic distribution and molecular diversity of HTNV, whole genome sequences of HTNV Large (L), Medium (M), and Small (S) segments were acquired from lung tissues of A. agrarius captured from 2003–2014. Consistent with the clinical incidence of HFRS established by the Korea Centers for Disease Control & Prevention (KCDC), the prevalence of HTNV in naturally infected mice in Gangwon province was lower than for Gyeonggi province. Whole genomic sequences of 34 HTNV strains were identified and a phylogenetic analysis showed geographic diversity of the virus in the limited areas. Reassortment analysis first suggested an occurrence of genetic exchange of HTNV genomes in nature, ROK. Conclusion/Significance This study is the first report to demonstrate the molecular prevalence of HTNV in Gangwon province. Whole genome sequencing of HTNV showed well-supported geographic lineages and the molecular diversity in the northern region of ROK due to a natural reassortment of HTNV genomes. These observations contribute to a better understanding of the genetic diversity and molecular evolution of hantaviruses. Also, the full-length of HTNV tripartite genomes will provide a database for phylogeographic analysis of spatial and temporal

  14. Complete genome sequence of a porcine astrovirus from South Korea.

    PubMed

    Lee, Sunhee; Jang, Guehwan; Lee, Changhee

    2015-07-01

    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.

  15. Epidemiology of Lung Cancer in Korea: Recent Trends

    PubMed Central

    Park, Ji Young

    2016-01-01

    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

  16. Epidemiology of Heart Failure in Korea: Present and Future

    PubMed Central

    Lee, Jung Hoon; Lim, Nam-Kyoo

    2016-01-01

    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

  17. Overview of the Epidemiology of Lower Urinary Tract Dysfunction in South Korea

    PubMed Central

    2016-01-01

    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

  18. Strengthening epidemiologic investigation of infectious diseases in Korea: lessons from the Middle East Respiratory Syndrome outbreak

    PubMed Central

    Lee, Changhwan; Ki, Moran

    2015-01-01

    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

  19. Complete genomic sequence analysis of norovirus isolated from South Korea.

    PubMed

    Lee, Gyu-Cheol; Jung, Gyoo Seung; Lee, Chan Hee

    2012-10-01

    The complete nucleotide and deduced amino acid sequences of the RNA genome of a recently isolated norovirus (NoV) from Korea, designated Hu/GII-4/CBNU2/2007/KR (CBNU2), were determined and characterized by phylogenetic comparison with several genetically diverse NoV sequences. The RNA genome of CBNU2 is 7,560 nucleotides in length, excluding the 3' poly (A) tract. It includes three open reading frames (ORFs): ORF1, which encodes the nonstructural polyprotein (5-5,104); ORF2, which encodes VP1 (5,085-6,707); and ORF3, which encodes VP2 (6,707-7,513). ORF2-based phylogenetic analysis revealed that CBNU2 belonged to the GII.4 genotype, the most prevalent genotype, and formed a cluster with NoVs isolated from Asian regions, between 2006 and 2008. Comparative analysis with the consensus sequence of 207 completely sequenced NoV genomes showed 47 mismatched nucleotides: 26 in ORF1, 14 in ORF2, and 7 in ORF3, resulting in 8 amino acid changes: 3 in ORF1, 2 in ORF2, and 3 in ORF3. Phylogenetic analysis with full genome ORF1, ORF2, and ORF3 nucleotide sequences obtained from CBNU2 and each of the other representative NoV genomes suggested that CBNU2 had not undergone recombination with any of the other NoVs. A SimPlot analysis further supported this finding.

  20. Molecular epidemiological investigation of Newcastle disease virus from domestic ducks in Korea.

    PubMed

    Lee, Eun-Kyoung; Jeon, Woo-Jin; Kwon, Jun-Hun; Yang, Chang-Bum; Choi, Kang-Seuk

    2009-03-01

    To expand the epidemiological understanding of Newcastle disease virus (NDV) found in domestic ducks in Korea, 14 NDV isolates from apparently healthy domestic ducks were biologically and genetically characterized. Thirteen and 1 isolates of NDV were categorized into lentogenic and velogenic viruses, respectively, based on in vivo pathogenicity tests. Twelve lentogenic viruses showed HA activity to horse RBCs, while 1 lentogenic virus and the velogenic virus were negative. Lentogenic viruses (n=13) had sequence motifs of (112)ERQERL(117) (n=1) or (112)GRQGRL(117) (n=12) at the F0 cleavage site, while the velogenic virus (n=1) had a sequence motif of (112)RRQKRF(117) at the same site. Phylogenetic analysis revealed that at least three distinct genotypes may exist in domestic ducks in Korea; one class I genotype (genotype 2), and two class II (genotypes I and VII) genotypes. The class I virus was most closely related to strains of genotype 2 which were isolated in birds from the USA, Germany and Denmark. Twelve lentogenic class II viruses were grouped together in genotype I, and were then divided into at least three clusters, namely Aomori-like, Ulster2C-like, and V4-like. The velogenic class II virus was assigned to genotype VII which represents viruses responsible for recent epidemics in many Asian countries including Korea. The epidemiological importance of domestic duck isolates of NDV in Korea is discussed.

  1. Epidemiology of Postherpetic Neuralgia in Korea: An Electronic Population Health Insurance System Based Study.

    PubMed

    Hong, Myong-Joo; Kim, Yeon-Dong; Cheong, Yong-Kwan; Park, Seon-Jeong; Choi, Seung-Won; Hong, Hyon-Joo

    2016-04-01

    Postherpetic neuralgia (PHN) is a disease entity defined as persistent pain after the acute pain of herpes zoster gradually resolves. It is associated with impaired daily activities, resulting in reduced quality of life. General epidemiological data on PHN is necessary for the effective management. However, data on the epidemiology of PHN in Korea is lacking. The aim of this study was to evaluate the epidemiological features of PHN in the general population.We used population-based medical data for 51,448,491 subscribers to the Health Insurance Service in the year of 2013 to analyze of PHN epidemiology in Korea, such as the incidence, regional distribution, seasonal variation, and healthcare resource utilization. Total number of patients and medical cost on PHN were analyzed from 2009 to 2013.Findings indicate that the incidence of PHN in Korea was 2.5 per 1000 person-years, which was strongly correlated with age and sex. There were no differences in seasonal variation or regional distribution. The medical cost increased steadily over the study period. When admitted to general hospitals, patients with PHN were mainly managed in the dermatology and anesthesiology departments.The incidence and prevalence rates of PHN in Koreans appear to be considerably higher compared to those in western populations, while the sex and age predisposition was similar. Considering that the pain associated with PHN can have a marked impact on a patient's quality of life resulting in a medicosocial economic burden, anesthesiology physicians have an important role in primary care in Korea. Future research on the cost-effectiveness of the management of PHN is needed. PMID:27057902

  2. About the Epidemiology and Genomics Research Program

    Cancer.gov

    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.

  3. Genomic epidemiology of artemisinin resistant malaria

    PubMed Central

    2016-01-01

    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

  4. Genomic epidemiology of artemisinin resistant malaria.

    PubMed

    2016-01-01

    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. PMID:26943619

  5. Novel Porcine Epidemic Diarrhea Virus Variant with Large Genomic Deletion, South Korea

    PubMed Central

    Park, Seongjun; Kim, Sanghyun; Song, Daesub

    2014-01-01

    Since 1992, porcine epidemic diarrhea virus (PEDV) has been one of the most common porcine diarrhea–associated viruses in South Korea. We conducted a large-scale investigation of the incidence of PEDV in pigs with diarrhea in South Korea and consequently identified and characterized a novel PEDV variant with a large genomic deletion. PMID:25424875

  6. Achalasia in Korea: an epidemiologic study using a national healthcare database.

    PubMed

    Kim, Eunkyung; Lee, Hongsub; Jung, Hye-Kyung; Lee, Kwang Jae

    2014-04-01

    Owing to the rarity of the disease, epidemiologic information on achalasia is limited. This study aimed to investigate the epidemiology and treatment patterns of achalasia in the population of Korea using a national healthcare database. The diagnostic code K22.0 of the International Classification of Diseases was used to identify cases of achalasia between 2007 and 2011. Treatment modalities for achalasia were identified using the electronic data interchange codes Q7642 or Q7641 for balloon dilation and QA421 or QA422 for esophago-cardiomyotomy. A total of 3,105 patients with achalasia (1,447 men; mean age, 52.5 yr) were identified between 2007 and 2011, indicating a prevalence of 6.29/100,000 (95% confidence interval [CI], 4.94-7.66) during this 5-yr period. A total of 191 incident cases of achalasia (82 men; mean age, 49.5 yr), which were not diagnosed as achalasia in the previous 4 yr, were detected in 2011, indicating an incidence of 0.39/100,000 (95% CI, 0.15-0.63) for that year. During the study period, balloon dilation therapy was performed a total of 975 times in 719 patients, and surgical esophago-cardiomyotomy was performed once per patient in 17 patients. This is the first population-based epidemiologic study of achalasia in Korea. PMID:24753707

  7. Complete Genome Sequence of Rotavirus Group C Isolated in South Korea

    PubMed Central

    Kim, Dong-Uk; Park, Kwi-Sung; Kim, Jae-Kyung

    2015-01-01

    Rotavirus group C is the major etiological agent associated with acute gastroenteritis in all human age groups. Here, we report the complete genome sequence of human group C rotavirus (GpC-RV) isolated in South Korea. PMID:26404599

  8. Epidemiology of Moyamoya Disease in Korea: Based on National Health Insurance Service Data.

    PubMed

    Kim, Tackeun; Lee, Heeyoung; Bang, Jae Seung; Kwon, O-Ki; Hwang, Gyojun; Oh, Chang Wan

    2015-06-01

    There have been a few studies reporting the epidemiology of moyamoya disease in Korea. Previous studies revealed relatively high prevalence and incidence of moyamoya disease in Korea and Japan. This study was designed to provide the latest epidemiologic information of moyamoya disease in Korea. We analyzed a database comprising of 50 million people covered in Korea by the National Health Insurance Service to calculate the prevalence. The incidence was estimated by eliminating the duplicated records of previous 3 years. We summarized the prevalence and incidence according to age, sex, and local distribution. In addition, the chronological changes were demonstrated with direct standardization using the 2010 population structure information. The standardized prevalence was 6.5 per 100000 persons in 2005, which was increased to 18.1 in 2013. In the same period, standardized incidence was increased from 2.7 to 4.3 per 100000 persons. The prevalence for men was 4.9 and 8.3 for women in 2005. In 2013, the prevalence had increased for men and women to 13.8 and 25.3, respectively. The incidence for men and women was 2.2 and 3.2, respectively, in 2005. It had increased to 3.5 and 5.7, respectively. The mean age of patients was 33.5 in 2005 and increased to 42.5 in 2013. The peak prevalent age group had shifted slightly to the older age groups, with chronologically consistent female predominance. The prevalence was highest in Jeollabuk province and lowest in Ulsan city.

  9. Epidemiology of Moyamoya Disease in Korea: Based on National Health Insurance Service Data

    PubMed Central

    Kim, Tackeun; Lee, Heeyoung; Bang, Jae Seung; Kwon, O-Ki; Hwang, Gyojun

    2015-01-01

    There have been a few studies reporting the epidemiology of moyamoya disease in Korea. Previous studies revealed relatively high prevalence and incidence of moyamoya disease in Korea and Japan. This study was designed to provide the latest epidemiologic information of moyamoya disease in Korea. We analyzed a database comprising of 50 million people covered in Korea by the National Health Insurance Service to calculate the prevalence. The incidence was estimated by eliminating the duplicated records of previous 3 years. We summarized the prevalence and incidence according to age, sex, and local distribution. In addition, the chronological changes were demonstrated with direct standardization using the 2010 population structure information. The standardized prevalence was 6.5 per 100000 persons in 2005, which was increased to 18.1 in 2013. In the same period, standardized incidence was increased from 2.7 to 4.3 per 100000 persons. The prevalence for men was 4.9 and 8.3 for women in 2005. In 2013, the prevalence had increased for men and women to 13.8 and 25.3, respectively. The incidence for men and women was 2.2 and 3.2, respectively, in 2005. It had increased to 3.5 and 5.7, respectively. The mean age of patients was 33.5 in 2005 and increased to 42.5 in 2013. The peak prevalent age group had shifted slightly to the older age groups, with chronologically consistent female predominance. The prevalence was highest in Jeollabuk province and lowest in Ulsan city. PMID:26180604

  10. Epidemiology of Lower Urinary Tract Symptoms: Emphasis on the Status in Korea

    PubMed Central

    Lee, Hakmin

    2014-01-01

    A comprehensive and correct understanding of epidemiologic finding about lower urinary tract symptoms (LUTS) is important for several reasons. First, LUTS are highly prevalent in both genders all around the world and are expected to be a major concern to physicians in the near future because of the rapid rise in the elderly population. Second, it is crucial to observe trends in prevalence when national health care policy is established. By using a Medline search with various terms related to LUTS and prevalence, a review of epidemiologic studies was undertaken with an emphasis on the status in Korea. Despite the suggestions made by the International Continence Society, the lack of uniform definitions and the lack of a unified threshold of symptoms are the biggest obstacles in epidemiologic study with regard to LUTS. Most Korean epidemiologic studies on LUTS have been reported since 2000 and reveal that the prevalences of specific clinical conditions, such as LUTS, benign prostatic hyperplasia, overactive bladder, and detrusor underactivity, are in line with prevalences in Western counties. However, the prevalence of nocturia is somewhat different from that in Western countries. Many epidemiologic studies of LUTS have provided us with valuable information and a better understanding of the clinical conditions. Given that the impact of these clinical conditions on quality of life and health care cost will be emphasized more in the near future, more studies on optimal management approaches to LUTS are needed on the basis of this knowledge. PMID:24868333

  11. Epidemiological characteristics of the first water-borne outbreak of cryptosporidiosis in Seoul, Korea.

    PubMed

    Moon, Shinje; Kwak, Wooseok; Lee, Sangwon; Kim, Won; Oh, Jaeyeon; Youn, Seung-Ki

    2013-07-01

    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.

  12. The Korea brassica genome project: a glimpse of the brassica genome based on comparative genome analysis with Arabidopsis.

    PubMed

    Yang, Tae-Jin; Kim, Jung-Sun; Lim, Ki-Byung; Kwon, Soo-Jin; Kim, Jin-A; Jin, Mina; Park, Jee Young; Lim, Myung-Ho; Kim, Ho-Il; Kim, Seog Hyung; Lim, Yong Pyo; Park, Beom-Seok

    2005-01-01

    A complete genome sequence provides unlimited information in the sequenced organism as well as in related taxa. According to the guidance of the Multinational Brassica Genome Project (MBGP), the Korea Brassica Genome Project (KBGP) is sequencing chromosome 1 (cytogenetically oriented chromosome #1) of Brassica rapa. We have selected 48 seed BACs on chromosome 1 using EST genetic markers and FISH analyses. Among them, 30 BAC clones have been sequenced and 18 are on the way. Comparative genome analyses of the EST sequences and sequenced BAC clones from Brassica chromosome 1 revealed their homeologous partner regions on the Arabidopsis genome and a syntenic comparative map between Brassica chromosome 1 and Arabidopsis chromosomes. In silico chromosome walking and clone validation have been successfully applied to extending sequence contigs based on the comparative map and BAC end sequences. In addition, we have defined the (peri)centromeric heterochromatin blocks with centromeric tandem repeats, rDNA and centromeric retrotransposons. In-depth sequence analyses of five homeologous BAC clones and an Arabidopsis chromosomal region reveal overall co-linearity, with 82% sequence similarity. The data indicate that the Brassica genome has undergone triplication and subsequent gene losses after the divergence of Arabidopsis and Brassica. Based on in-depth comparative genome analyses, we propose a comparative genomics approach for conquering the Brassica genome. In 2005 we intend to construct an integrated physical map, including sequence information from 500 BAC clones and integration of fingerprinting data and end sequence data of more than 100,000 BAC clones.

  13. Comparative study on the epidemiological aspects of enterohemorrhagic Escherichia coli infections between Korea and Japan, 2006 to 2010

    PubMed Central

    Lee, Won-Chang; Kwon, Young Hwan

    2016-01-01

    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

  14. A ROAD MAP FOR EFFICIENT AND RELIABLE HUMAN GENOME EPIDEMIOLOGY

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Network of investigators have begun sharing best practices, tools, and methods for analysis of associations between genetic variation and common diseases. A Network of Investigator Networks has been set up to drive the process, sponsored by the Human Genome Epidemiology Network. A workshop is planne...

  15. Epidemiology and Regional Distribution of Pediatric Unintentional Emergency Injury in Korea from 2010 to 2011.

    PubMed

    Jung, Jin Hee; Kim, Do Kyun; Jang, Hye Young; Kwak, Young Ho

    2015-11-01

    Injury is a leading cause of death and disability in children and adolescents worldwide. The purpose of the current study was to investigate the epidemiologic characteristics of the pediatric unintentional injuries presenting to the Korean emergency department (ED). We included unintentional injuries in patients aged < 20 yr. Data collected from January 2010 to December 2011 was extracted from the National Emergency Department Information System (NEDIS) of Korea. The NEDIS data included information on patient's age and gender, geographic location of the ED visits, mechanism of injuries; and clinical outcomes. Most (94.1%) injuries were unintentional while 5.9% were intentional. The rate of ED visit for pediatric unintentional injury was 6,097 per 100,000 and critical injury was 59.8 per 100,000 (< 20 yr habitants). The mortality rate was 5.4 per 100,000. The mortality rate of pediatric unintentional injuries was 0.1% including the prehospital death and ED death. Unintentional pediatric injuries occurred most commonly in those age 0-4 boys and girls and were predominantly caused by collisions. Male motorcyclists aged 15-19 yr formed a critical injury high-risk group. The rates of critical injury and mortality were highest in Jeju, Gangwon, Gwangju, and Jeonbuk than those in other regions. High-risk groups by age, gender, mechanism and region should be targeted to prevent pediatric injuries in Korea.

  16. Epidemiological findings of hepatitis B infection based on 1998 National Health and Nutrition Survey in Korea.

    PubMed Central

    Lee, Duk-Hee; Kim, Jin-Ha; Nam, Jung-Ja; Kim, Hye-Reon; Shin, Hai-Rim

    2002-01-01

    The purpose of this study was to investigate the epidemiological characteristics of hepatitis B virus (HBV) infection in Korea based on the 1998 National Health and Nutrition Survey. Study subjects consisted of 9,771 aged 10 yr or over, who were selected from across Korea using a stratified multistage probability sampling design. The prevalence of hepatitis B surface antigen (HBsAg) was compared by age, sex, residency, household income, education, family history, family size, and frequency of eating out. The prevalence of HBsAg was 5.1% (95% confidence interval (CI): 4.5-5.7) in males and 4.1% (95% CI: 3.6-4.6) in females with a low prevalence in those under 20 yr old. Generally, HBsAg seropositivity by administrative area was similar with the exception of Jeju province. HBsAg seropositivity of Jeju island was approximately three times higher in both men and women, as compared with the national average. HBsAg seropositivity by socioeconomic status unexpectedly showed a very consistent positive association in both gender. Comparing HBsAg seropositivity by the frequency of eating out, in both gender, the more frequent they ate out, the higher it was. Our study suggested that there might be another transmission route of HBV, which is possibly related to diet. PMID:12172038

  17. The Epidemiology and National Trends of Bearing Surface Usage in Primary Total Hip Arthroplasty in Korea

    PubMed Central

    Yoon, Pil Whan; Kim, Yunjung; Yoo, Seungmi; Lee, Sahnghoon; Kim, Hee Joong

    2016-01-01

    Background We analyzed the data for primary total hip arthroplasty (THA) in the Korean nationwide database to assess (1) the epidemiology and national trends of bearing surface usage in THAs and (2) the prevalence of each type of bearing surface according to age, gender, hospital type, primary payer, and hospital procedure volume. Methods A total of 30,881 THAs were analyzed using the Korean Health Insurance Review and Assessment Service database for 2007 through 2011. Bearing surfaces were sub-grouped according to device code for national health insurance claims and consisted of ceramic-on-ceramic (CoC), metal-on-polyethylene (MoP), ceramic-on-polyethylene (CoP), and metal-on-metal (MoM). The prevalence of each type of bearing surface was calculated and stratified by age, gender, hospital type, primary payer, and procedure volume of each hospital. Results CoC was the most frequently used bearing surface (76.7%), followed by MoP (11.9%), CoP (7.3%), and MoM (4.1%). The proportion of THAs using a CoC bearing surface increased steadily from 71.6% in 2007 to 81.4% in 2011, whereas the proportions using CoP, MoP, and MoM bearing surfaces decreased. The order of prevalence was identical to that in the general population regardless of age, gender, hospital type, primary payer, and hospital procedure volume. Conclusions The trends and epidemiology of bearing surface usage in THAs in Korea are different from those in other countries, and the CoC bearing surface is the most prevalent articulation. In future, the results of a large-scale study using nationwide data of THAs involving a CoC bearing surface will be reported in Korea. PMID:26929796

  18. Epidemiologic Parameters of the Middle East Respiratory Syndrome Outbreak in Korea, 2015

    PubMed Central

    Yoo, Jin-Hong; Choi, Jung-Hyun

    2016-01-01

    Background Epidemiologic parameters are important in planning infection control policies during the outbreak of emerging infections. Korea experienced an outbreak of Middle East Respiratory Syndrome coronavirus (MERS-CoV) infection in 2015, which was characterized by superspreading events in healthcare settings. We aimed to estimate the epidemiologic parameters over time during the outbreak to assess the effectiveness of countermeasures. Materials and Methods Publicly available data pertaining to the MERS outbreak in Korea were collected. We estimated the incubation periods of 162 cases whose sources of exposure were identified and the temporal trend was evaluated. Factors influencing incubation duration were analyzed. The generational reproduction number (Rg) and case reproduction number (Rc) were estimated over time. Results The estimated median incubation period was 7.4 days (95% CI, 6.9-8.0). Median incubation periods tended to be longer over time as the disease generation progressed: 6.16 days (95% CI, 5.38-6.97), 7.68 days (95% CI, 7.04-8.44), and 7.95 days (95% CI, 6.25-9.88) in the first, second, and third generations, respectively. The number of days of illness in the source cases at the time of exposure inversely correlated with the incubation periods in the receiving cases (HR 0.91 [95% CI, 0.84-0.99] per one illness day increase; P=0.026). This relationship was consistent (HR 0.83 [95% CI, 0.74-0.93] per one illness day increase) in the multivariable analysis incorporating clinical characteristics, the order of generation, and a link to superspreaders. Because the third generation cases were exposed to their source cases in the early stage (median one day) compared to the second generation cases (median 6 days), the temporal trend of incubation periods appears to be influenced by early isolation of symptomatic cases and reduction of potential exposure to source cases in the later stage. Rg declined rapidly from 28 to 0.23 in two generations. Rc dropped

  19. Epidemiology of brucellosis among cattle in Korea from 2001 to 2011.

    PubMed

    Yoon, Hachung; Moon, Oun-Kyong; Lee, Soo-Han; Lee, Won-Chang; Her, Moon; Jeong, Wooseog; Jung, Suk-Chan; Kim, Do-Soon

    2014-12-01

    In the present study, the outbreak patterns of bovine brucellosis in Korea from 2000 to 2011 were analyzed to understand the epidemiological evolution of this disease in the country. A total of 85,521 brucella reactor animals were identified during 14,215 outbreaks over the 12-year study period. The number of bovine brucellosis cases increased after 2003 and peaked in 2006 before decreasing thereafter. The majority of the bovine brucellosis cases were Korean native cattle, Han Woo. The numbers of human brucellosis cases and cattle outbreaks increased and decreased in the same pattern. The correlation coefficient for human and bovine cases per year was 0.96 (95% confidence interval = 0.86 ˜ 0.99; p < 10⁻³). The epidemiological characteristics of bovine brucellosis appeared to be affected by the intensity of eradication programs that mainly involved a test- and-slaughter policy. Findings from the present study were based on freely available statistics from web pages maintained by government agencies. This unlimited access to information demonstrates the usefulness of government statistics for continually monitoring the health of animal populations.

  20. Molecular Epidemiology and Genomics of Group A Streptococcus

    PubMed Central

    Bessen, Debra E.; McShan, W. Michael; Nguyen, Scott V.; Shetty, Amol; Agrawal, Sonia; Tettelin, Hervé

    2014-01-01

    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

  1. Complete Genome Sequence of Rehmannia Mosaic Virus Infecting Rehmannia glutinosa in South Korea

    PubMed Central

    Lim, Seungmo; Zhao, Fumei; Yoo, Ran Hee; Igori, Davaajargal; Jeong, Jae Cheol; Lee, Haeng-Soon; Kwak, Sang-Soo

    2016-01-01

    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

  2. Complete Genome Sequence of Ornithogalum Mosaic Virus Infecting Gladiolus spp. in South Korea

    PubMed Central

    Cho, Sang-Yun; Lim, Seungmo; Kim, Hongsup; Yi, Seung-In

    2016-01-01

    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

  3. Complete genome sequence of Klebsiella oxytoca M1, isolated from Manripo area of South Korea.

    PubMed

    Shin, Sang Heum; Roh, Hanseong; Kim, Juhyeok; Cho, Sukhyeong; Um, Youngsoon; Lee, Jinwon; Ryu, Yeon-Woo; Chong, Hyonyong; Yang, Kap-Seok

    2015-03-20

    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. PMID:25660421

  4. Complete Genome Sequence of Rehmannia Mosaic Virus Infecting Rehmannia glutinosa in South Korea.

    PubMed

    Lim, Seungmo; Zhao, Fumei; Yoo, Ran Hee; Igori, Davaajargal; Jeong, Jae Cheol; Lee, Haeng-Soon; Kwak, Sang-Soo; Moon, Jae Sun

    2016-01-28

    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.

  5. Complete Genome Sequence of Ornithogalum Mosaic Virus Infecting Gladiolus spp. in South Korea.

    PubMed

    Cho, Sang-Yun; Lim, Seungmo; Kim, Hongsup; Yi, Seung-In; Moon, Jae Sun

    2016-08-11

    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.

  6. Complete Genome Sequence of Nervous Necrosis Virus Isolated from Sevenband Grouper (Epinephelus septemfasciatus) in South Korea

    PubMed Central

    Kim, Jong-Oh; Kim, Wi-Sik; Cho, Jae-Kwon; Kim, Kyong-Min; Son, Maeng-Hyun

    2014-01-01

    The draft genome sequence of the nervous necrosis virus (NNV) SGYeosu08, isolated from sevenband grouper (Epinephelus septemfasciatus) in Yeosu, South Korea, was cloned and analyzed. The full-length RNA1 was a 3,103-nucleotide-encoding region of RNA-dependent RNA polymerase, and the RNA2 encoding a coat protein was 1,433 nucleotides in length. This genome sequence might be useful in the development of an accurate diagnostic tool. PMID:25502666

  7. Defining the Core Genome of Salmonella enterica Serovar Typhimurium for Genomic Surveillance and Epidemiological Typing.

    PubMed

    Fu, Songzhe; Octavia, Sophie; Tanaka, Mark M; Sintchenko, Vitali; Lan, Ruiting

    2015-08-01

    Salmonella enterica serovar Typhimurium is the most common Salmonella serovar causing foodborne infections in Australia and many other countries. Twenty-one S. Typhimurium strains from Salmonella reference collection A (SARA) were analyzed using Illumina high-throughput genome sequencing. Single nucleotide polymorphisms (SNPs) in 21 SARA strains ranged from 46 to 11,916 SNPs, with an average of 1,577 SNPs per strain. Together with 47 strains selected from publicly available S. Typhimurium genomes, the S. Typhimurium core genes (STCG) were determined. The STCG consist of 3,846 genes, a set that is much larger than that of the 2,882 Salmonella core genes (SCG) found previously. The STCG together with 1,576 core intergenic regions (IGRs) were defined as the S. Typhimurium core genome. Using 93 S. Typhimurium genomes from 13 epidemiologically confirmed community outbreaks, we demonstrated that typing based on the S. Typhimurium core genome (STCG plus core IGRs) provides superior resolution and higher discriminatory power than that based on SCG for outbreak investigation and molecular epidemiology of S. Typhimurium. STCG and STCG plus core IGR typing achieved 100% separation of all outbreaks compared to that of SCG typing, which failed to separate isolates from two outbreaks from background isolates. Defining the S. Typhimurium core genome allows standardization of genes/regions to be used for high-resolution epidemiological typing and genomic surveillance of S. Typhimurium.

  8. Epidemiologic characteristics of death by poisoning in 1991-2001 in Korea.

    PubMed

    Shin, Sang Do; Suh, Gil Joon; Rhee, Joong Eui; Sung, Joohon; Kim, Jaiyong

    2004-04-01

    The purpose of this study was to investigate the epidemiologic characteristics of the death by poisoning in Korea. We recoded the Death Certificates Database by injury based on the short version of the International Classification of External Causes of Injuries (ICECI). We evaluated the mortality rate by total injury and poisoning, and analyzed the mortality rate by age, gender, year and month, toxic agent, and intent. Adjusted odds ratios were calculated to evaluate the effects of socioeconomic factors on suicidal poisoning death. The total number of death cases by injury was 346,656. The proportion of death cases by injury decreased from 13.53% of all death cases in 1991 to 11.89% in 2001. However, the mortality rate by poisoning increased rapidly from 1998, and then remained stable. The number of suicidal poisoning deaths has gradually increased, and its mortality rate was 6.41 (per 100,000) in 2001. Major toxic agents were pesticides and herbicides (50.90%) in 2001. Adjusted odds ratios of suicidal poisoning versus other poisonings showed significant differences in education attainment, region, and marital status. In conclusion, the mortality rate by poisoning has increased, and the proportion of suicidal poisoning also has increased compared to that of accidental poisoning.

  9. A rapid whole genome sequencing and analysis system supporting genomic epidemiology (7th Annual SFAF Meeting, 2012)

    SciTech Connect

    FitzGerald, Michael

    2012-06-01

    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.

  10. A rapid whole genome sequencing and analysis system supporting genomic epidemiology (7th Annual SFAF Meeting, 2012)

    ScienceCinema

    FitzGerald, Michael [Broad Institute

    2016-07-12

    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.

  11. Whole genome sequence and genome annotation of Colletotrichum acutatum, causal agent of anthracnose in pepper plants in South Korea.

    PubMed

    Han, Joon-Hee; Chon, Jae-Kyung; Ahn, Jong-Hwa; Choi, Ik-Young; Lee, Yong-Hwan; Kim, Kyoung Su

    2016-06-01

    Colletotrichum acutatum is a destructive fungal pathogen which causes anthracnose in a wide range of crops. Here we report the whole genome sequence and annotation of C. acutatum strain KC05, isolated from an infected pepper in Kangwon, South Korea. Genomic DNA from the KC05 strain was used for the whole genome sequencing using a PacBio sequencer and the MiSeq system. The KC05 genome was determined to be 52,190,760 bp in size with a G + C content of 51.73% in 27 scaffolds and to contain 13,559 genes with an average length of 1516 bp. Gene prediction and annotation were performed by incorporating RNA-Seq data. The genome sequence of the KC05 was deposited at DDBJ/ENA/GenBank under the accession number LUXP00000000. PMID:27114908

  12. Whole-Genome Sequencing Analysis of Sapovirus Detected in South Korea.

    PubMed

    Choi, Hye Lim; Suh, Chang-Il; Park, Seung-Won; Jin, Ji-Young; Cho, Han-Gil; Paik, Soon-Young

    2015-01-01

    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.

  13. Incidence, epidemiology and evolution of reduced susceptibility to ciprofloxacin in Neisseria gonorrhoeae in Korea.

    PubMed

    Lee, Kyungwon; Chong, Yunsop; Erdenechemeg, L.; Soon Song, Kyung; Hun Shin, Kwang

    1998-01-01

    OBJECTIVE: To verify the decrease of susceptibility to ciprofloxacin in Neisseria gonorrhoeae, determine the size of the recently reported new beta-lactamase plasmid and explain the high prevalence of penicillinase-producing Neisseria gonorrhoeae (PPNG). METHODS: Gonococci were isolated from prostitutes in Korea. Antimicrobial susceptibility was tested by NCCLS disk diffusion and agar dilution methods. Plasmid was isolated by an alkaline lysis method. Patterns of Nhel-digested genomic DNA were compared after pulsed-field gel electrophoresis (PFGE). RESULTS: The minimum inhibitory concentration of ciprofloxacin for 50% of the isolates rose from 0.015 mg/L in 1993 to 0.12 mg/L in 1996. The proportion of PPNG remained at 70% or over during the 5-year period. The size of a novel beta-lactamase plasmid, first reported in 1994, was determined to be approximately 3.2 MDa, and 48% of the PPNG isolates contained it. Twelve of 50 isolates had the same PFGE pattern and nine others another pattern. CONCLUSION: The rapid decrease of fluoroquinolone-susceptible gonococci suggests that in the near future the drug may become less useful for gonorrhea treatment. The new 3.2-MDa plasmid may have been introduced as a result of the recent increase in overseas travel. The PFGE pattern suggests that high prevalence of PPNG may be due to dissemination of a few resistant clones among the high-risk groups. PMID:11864261

  14. Epidemiologic Aspects of Medical Retirement from the Republic of Korea Army due to Visual Impairment

    PubMed Central

    2016-01-01

    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. PMID:27051249

  15. The genomic and epidemiological dynamics of human influenza A virus

    PubMed Central

    Rambaut, Andrew; Pybus, Oliver G.; Nelson, Martha I.; Viboud, Cecile; Taubenberger, Jeffery K.; Holmes, Edward C.

    2008-01-01

    The evolutionary interaction between influenza A virus and the human immune system, manifest as ‘antigenic drift’ of the viral haemagglutinin, is one of the best described patterns in molecular evolution. However, little is known about the genome-scale evolutionary dynamics of this pathogen. Similarly, how genomic processes relate to global influenza epidemiology, in which the A/H3N2 and A/H1N1 subtypes co-circulate, is poorly understood. Here through an analysis of 1,302 complete viral genomes sampled from temperate populations in both hemispheres, we show that the genomic evolution of influenza A virus is characterized by a complex interplay between frequent reassortment and periodic selective sweeps. The A/H3N2 and A/H1N1 subtypes exhibit different evolutionary dynamics, with diverse lineages circulating in A/H1N1, indicative of weaker antigenic drift. These results suggest a sink-source model of viral ecology in which new lineages are seeded from a persistent influenza reservoir, which we hypothesize to be located in the tropics, to sink populations in temperate regions. PMID:18418375

  16. Protocol of a Thyroid Cancer Longitudinal Study (T-CALOS): a prospective, clinical and epidemiological study in Korea

    PubMed Central

    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

    2015-01-01

    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

  17. Genomic Signatures of Emerging Viruses: A New Era of Systems Epidemiology.

    PubMed

    Rasmussen, Angela L; Katze, Michael G

    2016-05-11

    Compared to classical epidemiologic methods, genomics can be used to precisely monitor virus evolution and transmission in real time across large, diverse populations. Integration of pathogen genomics with data about host genetics and global transcriptional responses to infection allows for comprehensive studies of population-level responses to infection and provides novel methods for predicting clinical outcomes. As genomic technologies become more accessible, these methods will redefine how emerging viruses are studied and outbreaks are contained. Here we review the existing and emerging genomic technologies that are enabling systems epidemiology and systems virology and making it possible to respond rapidly to emerging viruses such as Zika.

  18. Hepatitis A in Korea from 2011 to 2013: Current Epidemiologic Status and Regional Distribution.

    PubMed

    Moon, Shinje; Han, Jun Hee; Bae, Geun-Ryang; Cho, Enhi; Kim, Bongyoung

    2016-01-01

    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.

  19. [Epidemiological Studies On Clonorchis Sinensis Infection Along The Nam-River In Gyeongnam Province, Korea

    PubMed

    Bae, Kyoung Hoon; Ahn, Yung Kyum; Soh, Chin Thack; Tsutsumi, Hiroshi

    1983-12-01

    An epidemiological study on Clonorchis sinensis infection along the Nam-river (total length; 186km) flowing in Gyeongsang-nam-do, southern part of Korea, was carried out. Formalin-ether concentration technique and Stoll's egg counting method were employed to figure out the prevalence of C. sinensis infection. For the detection of cercariae from Parafossarulus sp., the snail host of C. sinensis, each snail was placed in aerated tap water, and examined for expelled cercariae. For observing the metacercariae the fresh water fish favorably eaten in raw conditions were prepared by means of pressing the muscles between tow slide glasses and/or by digesting them with artificial gastric juice. The fresh water fish were fed to the rabbits to get the worms and to identify the morphology of adult C. sinensis. The results are summarized as follows: 1. Overall prevalence of C. sinensis infection was 38.7% form 5,291 examinees; 44.1% (1,408 out of 3,196) in male and 30.4% (637 out of 2,095) in female. 2. The prevalence rates were 42.0% at the upper stream, 41.2% around the vicinity of Jinyang-lake, 34.2% at Jinju city, 34.2% at middle stream and 40.3% at down stream regions, respectively. 3. By age, the highest positive rate (53.4~54.3%) was observed in 30 to 59 years of age. In this age group, the rate in males was 59.7~62.2%, and in females 42.2~44.4%. In the age group of less than 19years it was 7.5~20.9%. 4. By social strata, the positive rate was 16.5% in the primary school children, 22.6% in school students, 46.2% in teachers and local officers and 49.6% in the general inhabitants. 5. The quantitative examinations with the stool collected from clonorchiasis cases revealed that the light infection (less than 4,000/EPG) was 53.6%, moderate infection (4,001~10,000/EPG) 30.3% and heavy infection (more than 10,001/EPG) 16.1, respectively. More than half of total cases examined were light infection, and 73.2% of female examinees were lightly infected with this fluke. 6. The

  20. Complete Nucleotide Sequences and Genome Organization of Two Pepper Mild Mottle Virus Isolates from Capsicum annuum in South Korea.

    PubMed

    Choi, Seung-Kook; Choi, Gug-Seoun; Kwon, Sun-Jung; Yoon, Ju-Yeon

    2016-05-19

    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.

  1. Complete Nucleotide Sequences and Genome Organization of Two Pepper Mild Mottle Virus Isolates from Capsicum annuum in South Korea

    PubMed Central

    Choi, Seung-Kook; Choi, Gug-Seoun; Kwon, Sun-Jung

    2016-01-01

    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

  2. Complete genome sequence of Seoul virus isolated from Rattus norvegicus in the Democratic People's Republic of Korea.

    PubMed

    Yao, Li-Si; Qin, Cheng-Feng; Pu, Yun; Zhang, Xiao-Long; Liu, Yong-Xian; Liu, Yang; Cao, Xiao-mei; Deng, Yong-Qiang; Wang, Jing; Hu, Kong-Xin; Xu, Bao-Liang

    2012-12-01

    Seoul virus (SEOV) is responsible for 25% of cases of hemorrhagic fever with renal syndrome in Asia. Here we report the complete genome of strain DPRK08. The sequence information provided here is useful for understanding the molecular character of SEOV in the Democratic People's Republic of Korea (DPRK) and the circulation of SEOV in East Asia.

  3. Complete Genome Sequence of Chinese Yam Necrotic Mosaic Virus from Dioscorea opposita in the Republic of Korea

    PubMed Central

    Son, Chang-Gi; Kwon, Joong-Bae; Nam, Hyo-Hun; Kim, Yeongtae; Lee, Su-Heon; Zhao, Fumei; Moon, Jae Sun

    2016-01-01

    The complete genome sequence of Chinese yam necrotic mosaic virus (ChYNMV) consisting of 8,213 nucleotides containing one open reading frame was determined by the transcriptome data generated from Discorea opposita. This is the first report of the complete nucleotide sequence of ChYNMV from Dioscorea opposita in the Republic of Korea. PMID:27492000

  4. Complete Genome Sequence of Chinese Yam Necrotic Mosaic Virus from Dioscorea opposita in the Republic of Korea.

    PubMed

    Lee, Joong-Hwan; Son, Chang-Gi; Kwon, Joong-Bae; Nam, Hyo-Hun; Kim, Yeongtae; Lee, Su-Heon; Zhao, Fumei; Moon, Jae Sun

    2016-08-04

    The complete genome sequence of Chinese yam necrotic mosaic virus (ChYNMV) consisting of 8,213 nucleotides containing one open reading frame was determined by the transcriptome data generated from Discorea opposita This is the first report of the complete nucleotide sequence of ChYNMV from Dioscorea opposita in the Republic of Korea.

  5. Genome Sequence of Porphyrobacter dokdonensis DSW-74T, Isolated from Seawater off Dokdo in the East Sea (Sea of Korea)

    PubMed Central

    Song, Ju Yeon; Hong, Juhye; Kwak, Min-Jung; Kwon, Soon-Kyeong

    2016-01-01

    Porphyrobacter dokdonensis strain DSW-74, isolated from seawater off of Dokdo, Republic of Korea, is a member of the family Erythrobacteraceae. In this study, the genome sequence of DSW-74 was determined using the Illumina HiSeq 2000 platform and assembled into 11 contigs. Its genome is approximately 3.0 Mb with a G+C content of 64.8%, in which 2,875 protein-coding sequences and 47 RNA genes were predicted. PMID:27587820

  6. Genome Sequence of Porphyrobacter dokdonensis DSW-74T, Isolated from Seawater off Dokdo in the East Sea (Sea of Korea).

    PubMed

    Song, Ju Yeon; Hong, Juhye; Kwak, Min-Jung; Kwon, Soon-Kyeong; Kim, Jihyun F

    2016-01-01

    Porphyrobacter dokdonensis strain DSW-74, isolated from seawater off of Dokdo, Republic of Korea, is a member of the family Erythrobacteraceae In this study, the genome sequence of DSW-74 was determined using the Illumina HiSeq 2000 platform and assembled into 11 contigs. Its genome is approximately 3.0 Mb with a G+C content of 64.8%, in which 2,875 protein-coding sequences and 47 RNA genes were predicted. PMID:27587820

  7. Genome Sequence of Porphyrobacter dokdonensis DSW-74T, Isolated from Seawater off Dokdo in the East Sea (Sea of Korea).

    PubMed

    Song, Ju Yeon; Hong, Juhye; Kwak, Min-Jung; Kwon, Soon-Kyeong; Kim, Jihyun F

    2016-09-01

    Porphyrobacter dokdonensis strain DSW-74, isolated from seawater off of Dokdo, Republic of Korea, is a member of the family Erythrobacteraceae In this study, the genome sequence of DSW-74 was determined using the Illumina HiSeq 2000 platform and assembled into 11 contigs. Its genome is approximately 3.0 Mb with a G+C content of 64.8%, in which 2,875 protein-coding sequences and 47 RNA genes were predicted.

  8. Molecular epidemiology of norovirus in asymptomatic food handlers in Busan, Korea, and emergence of genotype GII.17.

    PubMed

    Koo, Hee Soo; Lee, Mi Ok; Ku, Pyeong Tae; Hwang, Su Jeong; Park, Dong Ju; Baik, Hyung Suk

    2016-10-01

    The molecular epidemiology of norovirus infections was studied in food handlers without any symptoms from January to December 2015 in Busan city, Korea. A total of 2,174 fecal specimens from asymptomatic food handlers were analyzed, and 2.3% (49/2,174) were norovirus-positive. Fourteen of 335 samples (4.2%) were positive in January; fifteen of 299 samples (5.0%) in February, and seven of 189 samples (3.7%) in December. However, norovirus was rarely detected in other months. From sequencing analysis, 11 genotypes (five GI and six GII genotypes) were detected. Among the 42 capid gene sequences identified, 14 were from the GI genogroup, while 28 were from the GII genogroup. The most commonly detected genotype was GII.17, comprising 15 (35.7%) of positive samples. From January 2012 to December 2015, 5,138 samples were collected from gastroenteritis patients and outbreaks in Busan. The most detected genotype in 2012, 2013, and 2014 was GII.4 (121, 24, and 12 cases, respectively), but in 2015, GII.17 (25 cases) was the most common. The GII.4 genotype was the major cause of acute gastroenteritis from 2012 to 2014, but the GII.17 genotype became the most prevalent cause in 2015. Continued epidemiological surveillance of GII.17 is needed, together with assessment of the risk of norovirus infection. PMID:27687231

  9. A study testing the usefulness of a dish-based food-frequency questionnaire developed for epidemiological studies in Korea.

    PubMed

    Kim, Young Ok; Kim, Mi Kyung; Lee, Sang-Ah; Yoon, Young Mi; Sasaki, Satoshi

    2009-04-01

    The purpose of the present study was to test the usefulness of dish items selected in developing a dish-based FFQ (DFFQ) to be used for epidemiological studies in Korea. The dietary data of 6817 subjects from the 2001 Korean National Health and Nutrition Examination Survey were used for the analysis. The 24 h recall method was employed for the dietary survey. Initially, ninety-five dish items were selected in developing the DFFQ based on consumption frequency, contribution of selected nutrients and coverage of between-person variations. The usefulness of the selected ninety-five dish items was tested based on their degree of contribution in supplying nutrients in the cumulative percentage contribution (cPC), as well as on their degree of explanation for between-person variation in the cumulative regression coefficient (cMRC). According to the results, the ninety-five selected dish items accounted for an average of 92.3 % of seventeen nutrients consumed by the study subjects based on cPC estimation. The top twenty items among the ninety-five dish items covered 70 to 91 % of the between-person variation for the seventeen nutrients based on cMRC estimation. Thus, the results suggest that the ninety-five items would be useful in developing a FFQ for use in epidemiological studies of Koreans, within less than 10 % underestimation. PMID:18786277

  10. Whole genome multilocus sequence typing as an epidemiologic tool for Yersinia pestis.

    PubMed

    Kingry, Luke C; Rowe, Lori A; Respicio-Kingry, Laurel B; Beard, Charles B; Schriefer, Martin E; Petersen, Jeannine M

    2016-04-01

    Human plague is a severe and often fatal zoonotic disease caused by Yersinia pestis. For public health investigations of human cases, nonintensive whole genome molecular typing tools, capable of defining epidemiologic relationships, are advantageous. Whole genome multilocus sequence typing (wgMLST) is a recently developed methodology that simplifies genomic analyses by transforming millions of base pairs of sequence into character data for each gene. We sequenced 13 US Y. pestis isolates with known epidemiologic relationships. Sequences were assembled de novo, and multilocus sequence typing alleles were assigned by comparison against 3979 open reading frames from the reference strain CO92. Allele-based cluster analysis accurately grouped the 13 isolates, as well as 9 publicly available Y. pestis isolates, by their epidemiologic relationships. Our findings indicate wgMLST is a simplified, sensitive, and scalable tool for epidemiologic analysis of Y. pestis strains. PMID:26778487

  11. Preliminary epidemiologic assessment of MERS-CoV outbreak in South Korea, May–June 2015

    PubMed Central

    Cowling, Benjamin J; Park, Minah; Fang, Vicky J; Wu, Peng; Leung, Gabriel M; Wu, Joseph T

    2015-01-01

    South Korea is experiencing the largest outbreak of Middle East respiratory syndrome coronavirus infections outside the Arabian Peninsula, with 166 laboratory-confirmed cases, including 24 deaths as of 19 June 2015. We estimated that the mean incubation period was 6.7 days and the mean serial interval 12.6 days. We found it unlikely that infectiousness precedes symptom onset. Based on currently available data, we predict an overall case fatality risk of 21.3% (95% credible interval: 14%–31%). PMID:26132767

  12. Genomic fluidity and pathogenic bacteria: applications in diagnostics, epidemiology and intervention.

    PubMed

    Ahmed, Niyaz; Dobrindt, Ulrich; Hacker, Jörg; Hasnain, Seyed E

    2008-05-01

    The increasing availability of DNA-sequence information for multiple pathogenic and non-pathogenic variants of individual bacterial species has indicated that both DNA acquisition and genome reduction have important roles in genome evolution. Such genomic fluidity, which is found in human pathogens such as Escherichia coli, Helicobacter pylori and Mycobacterium tuberculosis, has important consequences for the clinical management of the diseases that are caused by these pathogens and for the development of diagnostics and new molecular epidemiological methods.

  13. Bacterial genomic epidemiology, from local outbreak characterization to species-history reconstruction

    PubMed Central

    Gaiarsa, Stefano; De Marco, Leone; Comandatore, Francesco; Marone, Piero; Bandi, Claudio; Sassera, Davide

    2015-01-01

    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

  14. Epidemiology of Campylobacter jejuni Outbreak in a Middle School in Incheon, Korea

    PubMed Central

    Kim, Na-Yeon; Cho, Nam-Gue; Kim, Jung-Hee; Kang, Young-Ah; Lee, Ha-Gyung

    2010-01-01

    On July 6, 2009, an outbreak of gastroenteritis occurred among middle school students in Incheon. An investigation to identify the source and describe the extent of the outbreak was conducted. A retrospective cohort study among students, teachers, and food handlers exposed to canteen food in the middle school was performed. Using self-administered questionnaires, information was collected concerning on symptoms, days that canteen food was consumed, and food items consumed. Stool samples were collected from 66 patients and 11 food handlers. The catering kitchen was inspected and food samples were taken. Of the 791 people who ate canteen food, 92 cases became ill, representing an attack rate of 11.6%. Thirty-one (40.3%) of the 77 stool specimens were positive for Campylobacter jejuni. Interviews with kitchen staff indicated the likelihood that undercooked chicken was provided. This is the first recognized major C. jejuni outbreak associated with contaminated chicken documented in Korea. PMID:21060748

  15. [The Human Genome Project, genetic viability and genetic epidemiology].

    PubMed

    Hagymási, Krisztina; Tulassay, Zsolt

    2005-12-18

    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.

  16. Leveraging epidemiologic and clinical collections for genomic studies of complex traits

    PubMed Central

    Crawford, Dana C.; Goodloe, Robert; Farber-Eger, Eric; Boston, Jonathan; Pendergrass, Sarah A.; Haines, Jonathan L.; Ritchie, Marylyn D.; Bush, William S.

    2015-01-01

    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

  17. Epidemiology of egg drop syndrome virus in ducks from South Korea.

    PubMed

    Cha, S-Y; Kang, M; Park, C-K; Choi, K-S; Jang, H-K

    2013-07-01

    Egg drop syndrome virus (EDSV) is an important pathogen of poultry that decreases egg production in chickens and causes respiratory disease in goslings. In 2011, we obtained serum samples from 139 domestic Pekin ducks, 416 one-day-old Pekin ducklings, and 75 wild ducks (67 mallards and 8 pintails) to survey their exposure to EDSV. A total of 123 of 139 sera (88.5%) from Pekin ducks, 396 of the ducklings (95.2%), and 16 of 67 mallards (23.9%) were positive. Field cases of EDSV in wild and domestic ducks were investigated. Six cases from domestic Pekin ducks were identified by PCR detection and were used for virus isolation and molecular analysis. Phylogenetic analyses of the partial hexon and full fiber genes showed that the D11-JW-012 and D11-JW-017 strains among 6 isolates belonged to different clusters compared with other known strains including the 127 strain. We assessed cell growth efficiency by hemagglutination (HA) titers and cytopathic effects in duck embryo liver cells and chicken embryo liver (CEL) cells to investigate host adaptation. The D11-JW-017 strain propagated more in chicken embryo liver than the D11-JW-012 strain and the field isolate from chickens. Our results demonstrate the high prevalence of EDSV in wild and domestic ducks in South Korea and provide information on EDSV from ducks that showed variable adaptability in chickens. PMID:23776265

  18. Epidemiology of egg drop syndrome virus in ducks from South Korea.

    PubMed

    Cha, S-Y; Kang, M; Park, C-K; Choi, K-S; Jang, H-K

    2013-07-01

    Egg drop syndrome virus (EDSV) is an important pathogen of poultry that decreases egg production in chickens and causes respiratory disease in goslings. In 2011, we obtained serum samples from 139 domestic Pekin ducks, 416 one-day-old Pekin ducklings, and 75 wild ducks (67 mallards and 8 pintails) to survey their exposure to EDSV. A total of 123 of 139 sera (88.5%) from Pekin ducks, 396 of the ducklings (95.2%), and 16 of 67 mallards (23.9%) were positive. Field cases of EDSV in wild and domestic ducks were investigated. Six cases from domestic Pekin ducks were identified by PCR detection and were used for virus isolation and molecular analysis. Phylogenetic analyses of the partial hexon and full fiber genes showed that the D11-JW-012 and D11-JW-017 strains among 6 isolates belonged to different clusters compared with other known strains including the 127 strain. We assessed cell growth efficiency by hemagglutination (HA) titers and cytopathic effects in duck embryo liver cells and chicken embryo liver (CEL) cells to investigate host adaptation. The D11-JW-017 strain propagated more in chicken embryo liver than the D11-JW-012 strain and the field isolate from chickens. Our results demonstrate the high prevalence of EDSV in wild and domestic ducks in South Korea and provide information on EDSV from ducks that showed variable adaptability in chickens.

  19. Assessment of radiation exposure from cesium-137 contaminated roads for epidemiological studies in Seoul, Korea

    PubMed Central

    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

    2015-01-01

    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

  20. Genomic Footprints in Selected and Unselected Beef Cattle Breeds in Korea.

    PubMed

    Lim, Dajeong; Strucken, Eva M; Choi, Bong Hwan; Chai, Han Ha; Cho, Yong Min; Jang, Gul Won; Kim, Tae-Hun; Gondro, Cedric; Lee, Seung Hwan

    2016-01-01

    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

  1. Genomic Footprints in Selected and Unselected Beef Cattle Breeds in Korea.

    PubMed

    Lim, Dajeong; Strucken, Eva M; Choi, Bong Hwan; Chai, Han Ha; Cho, Yong Min; Jang, Gul Won; Kim, Tae-Hun; Gondro, Cedric; Lee, Seung Hwan

    2016-01-01

    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.

  2. Genomic Footprints in Selected and Unselected Beef Cattle Breeds in Korea

    PubMed Central

    Choi, Bong Hwan; Chai, Han Ha; Cho, Yong Min; Jang, Gul Won; Kim, Tae-Hun; Gondro, Cedric; Lee, Seung Hwan

    2016-01-01

    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

  3. Complete chloroplast genome of Prunus yedoensis Matsum.(Rosaceae), wild and endemic flowering cherry on Jeju Island, Korea.

    PubMed

    Cho, Myong-Suk; Hyun Cho, Chung; Yeon Kim, Su; Su Yoon, Hwan; Kim, Seung-Chul

    2016-09-01

    The complete chloroplast genome sequences of the wild flowering cherry, Prunus yedoensis Matsum., which is native and endemic to Jeju Island, Korea, is reported in this study. The genome size is 157 786 bp in length with 36.7% GC content, which is composed of LSC region of 85 908 bp, SSC region of 19 120 bp and two IR copies of 26 379 bp each. The cp genome contains 131 genes, including 86 coding genes, 8 rRNA genes and 37 tRNA genes. The maximum likelihood analysis was conducted to verify a phylogenetic position of the newly sequenced cp genome of P. yedoensis using 11 representatives of complete cp genome sequences within the family Rosaceae. The genus Prunus exhibited monophyly and the result of the phylogenetic relationship agreed with the previous phylogenetic analyses within Rosaceae. PMID:26329800

  4. Epidemiology of the Foot-and-Mouth Disease Serotype O Epidemic of November 2010 to April 2011 in the Republic Of Korea.

    PubMed

    Yoon, H; Yoon, S-S; Kim, Y-J; Moon, O-K; Wee, S-H; Joo, Y-S; Kim, B

    2015-06-01

    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.

  5. Whole genome sequencing: the future for molecular epidemiological studies on aquatic pathogens

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The advent of next generation sequencing (NGS) has transformed our ability to analyze the genomic content of isolated strains and communities of microorganisms. An important application of the new technology is for molecular epidemiology, as single sequencing reactions can generate nearly complete ...

  6. Epidemiologic differences of four major respiratory viruses between children, adolescents, and adults in Korea.

    PubMed

    Seo, Yu Bin; Cheong, Hee Jin; Song, Joon Young; Noh, Ji Youn; Kim, In Seon; Song, Dae Jin; Kim, Woo Joo

    2014-11-01

    The purpose of this study was to investigate the epidemiology of four major respiratory viruses among the Korean population. This retrospective study was conducted over four years, from January 2005 to December 2008. Among a total of 23,806 specimens, 5512 virus isolates underwent culture for influenza A and B viruses (IFA/B), parainfluenza virus (PIV), respiratory syncytial virus (RSV), and adenovirus (ADV). Patients were divided into two groups: children/adolescents and adults. The viruses detected in specimens from children/adolescents included PIV (7.8%), RSV (7.3%), ADV (4.0%), IFA (2.9%), and IFB (2.2%). In adults, IFB (5.6%), IFA (4.4%), RSV (1.1%), PIV (0.5%), and ADV (0.2%) were detected, thus demonstrating two distinct patterns of virus infection. Influenza viruses had similar seasonal patterns and periods of infection among children/adolescents and adults; however, the isolation rate in adults was slightly higher than that in children and adolescents. Correlation coefficient analysis based on weekly seasonal patterns indicated that influenza viruses were detected a week earlier in children than in adults. RSV, PIV, and ADV did not show similar trends between the two age groups due to low detection rates and sporadic isolations among adult patients. Of note, different respiratory viruses should be considered depending on patient age when a clinical respiratory viral infection is suspected. Furthermore, in the case of influenza, a preceding epidemic among a pediatric population could be useful to predict a subsequent epidemic among adults.

  7. [Epidemiological Studies Of Clonorchis Sinensis In Mangyeong Riverside Areas In Korea

    PubMed

    Rhee, Jae Ku; Baek, Byeong Kirl; Lee, Sang Bork; Koh, Hong Bum

    1983-12-01

    In an attempt to clarify the epidemiological feature of C. sinensis in Mangyeong riverside area, the prevalence of clonorchiasis, infestation rate of the cercariae in Parafossarulus manchouricus, and detection rate of the metacercariae in fresh-water fishes were investigated from March 1 to September 30, 1983 at the upper, middle and lower reaches of the river. The results obtained were summarized as follows:Detection rate of C. sinensis egg among inhabitants was 8.2 % out of a total of 1,266 persons. but the differences in detection rates were not statistically signifcant among upper, middle and 1ower reaches. According to sex, the detection rates were 10.3 % in male and 6.1 % in female (p<0.05), but by age groups, increases of the rates were observed as increase in age (p<0.05). Out of a total of 380 fresh-water fishes of 32 different species, 93 fishes (25 %) of 12 species were found positive with Clonorchis metacercariae, and there were differences in infection rates of the metacercariae among the fishes in 3 parts of the river; 11 % in upper, 35 % in middle, and 34 % in lower reaches respectively. The metacercarial detection rates from various fishes were 97 % in Pseudorasbora parva, Cultriculus eigenmanni (85 %), Gnathopogon strigatus (67 %), Microphysogobio yaluensis (50 %), Gnathopogon coreanus (47 %), Pungtungia herzi(44 %), Abbottina rivularis (40 %), Moroco oxycephalus (33 %), Coreoleuciscus splendidus (32 %), Gnathopogon majimae (26 %), Rhodeus ocellatus (7 %), and Aphyocypris chinensis (3 %) respectively. Although very few P. manchouricus were collected at upper reach, 12 snails (0.7 %) among a total of 1,713 were found infected with Clonorchis cercariae. Also the cercariae of Echinochasmus japonicus (7.99 %), Lexogenes liberum (0.99 %), Cyathocotyle orientalis (0.75 %), Exorchis oviformis (0.23 %) and Asymphylodora japonica (0.05 %) were detected from the snails.

  8. Retrospective analysis of the epidemiologic literature, 1990–2015, on wildlife-associated diseases from the Republic of Korea

    USGS Publications Warehouse

    Hwang, Jusun; Lee, Kyunglee; Kim, Young-Jun; Sleeman, Jonathan M.; Lee, Hang

    2016-01-01

    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

  9. Chemoprophylaxis and the epidemiological characteristics of re-emergent P. vivax malaria in the Republic of Korea.

    PubMed Central

    Kim, Changsoo; Shin, Dong Chun; Yong, Tai Soon; Oh, Dae Kyu; Kim, Rock Kwon; Park, Keeho; Suh, I. L.

    2006-01-01

    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 2 months after the last day of exposure to risk of malaria, respectively. FINDINGS: Of these cases, 634 (72.0%) had received chemoprophylaxis, and 324 (28.0%) had not. Cases occurred mostly in summer, with a peak in July-August. Stratification by chemoprophylaxis history revealed different times to onset. Early primary attacks were more prevalent in the group not receiving chemoprophylaxis, while in the group receiving chemoprophylaxis most cases were late primary attacks. Of the latter, 312 out of 461 (67.7%) did not take primaquine regularly. After treatment of the first attack, 14 (1.2%) of 1158 were re-treated; all re-treated cases were cured using the same doses and regimen used for the first treatment. CONCLUSION: In ROK, the increase in late primary episodes of re-emergent P. vivax malaria is associated with the use of antimalarial chemoprophylaxis. PMID:17128363

  10. Genomic epidemiology of multidrug-resistant Mycobacterium tuberculosis during transcontinental spread.

    PubMed

    Coscolla, Mireia; Barry, Pennan M; Oeltmann, John E; Koshinsky, Heather; Shaw, Tambi; Cilnis, Martin; Posey, Jamie; Rose, Jordan; Weber, Terry; Fofanov, Viacheslav Y; Gagneux, Sebastien; Kato-Maeda, Midori; Metcalfe, John Z

    2015-07-15

    The transcontinental spread of multidrug-resistant (MDR) tuberculosis is poorly characterized in molecular epidemiologic studies. We used genomic sequencing to understand the establishment and dispersion of MDR Mycobacterium tuberculosis within a group of immigrants to the United States. We used a genomic epidemiology approach to study a genotypically matched (by spoligotype, IS6110 restriction fragment length polymorphism, and mycobacterial interspersed repetitive units-variable number of tandem repeat signature) lineage 2/Beijing MDR strain implicated in an outbreak of tuberculosis among refugees in Thailand and consecutive cases within California. All 46 MDR M. tuberculosis genomes from both Thailand and California were highly related, with a median difference of 10 single-nucleotide polymorphisms (SNPs). The Wat Tham Krabok (WTK) strain is a new sequence type distinguished from all known Beijing strains by 55 SNPs and a genomic deletion (Rv1267c) associated with increased fitness. Sequence data revealed a highly prevalent MDR strain that included several closely related but distinct allelic variants within Thailand, rather than the occurrence of a single outbreak. In California, sequencing data supported multiple independent introductions of WTK with subsequent transmission and reactivation within the state, as well as a potential super spreader with a prolonged infectious period. Twenty-seven drug resistance-conferring mutations and 4 putative compensatory mutations were found within WTK strains. Genomic sequencing has substantial epidemiologic value in both low- and high-burden settings in understanding transmission chains of highly prevalent MDR strains. PMID:25601940

  11. Isolation and genomic characterization of Chaoyang virus strain ROK144 from Aedes vexans nipponii from the Republic of Korea.

    PubMed

    Lee, John S; Grubaugh, Nathan D; Kondig, John P; Turell, Michael J; Kim, Heung-Chul; Klein, Terry A; O'Guinn, Monica L

    2013-01-20

    During June 2003, mosquito surveillance was conducted at a US Army installation and a US Military training site 2 km south of the demilitarized zone, Republic of Korea. Mosquitoes were collected using Mosquito Magnets™, sorted to species, and assayed for the presence of arboviruses. From the 3,149 mosquitoes that were sorted into 126 pools, one Aedes vexans nipponii pool (out of 73 pools) tested positive for flavivirus RNA by reverse transcription-PCR. After isolation from C6/36 cell culture supernatant, the viral genome was sequenced and found to be 98.9% related to Chaoyang virus, a potential arthropod-specific flavivirus. This report details the first identification of Chaoyang virus in the Republic of Korea and highlights its relationship to other flaviviruses.

  12. Using Epidemiology and Genomics to Understand Osteosarcoma Etiology

    PubMed Central

    Savage, Sharon A.; Mirabello, Lisa

    2011-01-01

    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

  13. Large genomic rearrangement of BRCA1 and BRCA2 genes in familial breast cancer patients in Korea.

    PubMed

    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

    2014-06-01

    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.

  14. Global Genomic Epidemiology of Salmonella enterica Serovar Typhimurium DT104.

    PubMed

    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

    2016-04-01

    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.

  15. Global Genomic Epidemiology of Salmonella enterica Serovar Typhimurium DT104.

    PubMed

    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

    2016-04-01

    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. PMID:26944846

  16. Global Genomic Epidemiology of Salmonella enterica Serovar Typhimurium DT104

    DOE PAGESBeta

    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.; et al

    2016-03-04

    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

  17. Global Genomic Epidemiology of Salmonella enterica Serovar Typhimurium DT104

    PubMed Central

    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.

    2016-01-01

    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

  18. Homology differences between complete Sacbrood virus genomes from infected Apis mellifera and Apis cerana honeybees in Korea.

    PubMed

    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

    2016-04-01

    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. PMID:26810400

  19. Homology differences between complete Sacbrood virus genomes from infected Apis mellifera and Apis cerana honeybees in Korea.

    PubMed

    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

    2016-04-01

    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.

  20. Population Stratification in the Context of Diverse Epidemiologic Surveys Sans Genome-Wide Data

    PubMed Central

    Oetjens, Matthew T.; Brown-Gentry, Kristin; Goodloe, Robert; Dilks, Holli H.; Crawford, Dana C.

    2016-01-01

    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

  1. Population Stratification in the Context of Diverse Epidemiologic Surveys Sans Genome-Wide Data.

    PubMed

    Oetjens, Matthew T; Brown-Gentry, Kristin; Goodloe, Robert; Dilks, Holli H; Crawford, Dana C

    2016-01-01

    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 for

  2. Epidemiologic implications of changes in the influenza virus genome.

    PubMed

    Kendal, A P

    1987-06-19

    Among the molecular maneuvers that enable the influenza virus to survive are antigenic variation and functional alterations. Two kinds of minor antigenic variations, producing new strains within type A virus subtypes, have been discovered: antigenic drift, in which the amino acid sequences of the antigens are changed; and antigenic camouflage, in which the antigens are glycosylated. Both kinds of variation are caused by mutations in the viral genome. These mutations produce slightly changed antigens, which many existing antibodies cannot recognize. Major antigenic variations (so-called antigenic shift) are produced by gene reassortment. Two subtypes, coinfecting a host, can reassort their eight ribonucleoprotein gene segments into as many as 256 different combinations. Such recombinations can produce new viruses with the potential for transmission in humans, but whose surface antigens are completely unmatched by antibodies in the population, permitting a pandemic to occur. Functional changes, caused by mutations, alter the interactions between the virus and the host, including virus binding to host receptor sites and fusion of viral and host membranes. All these mechanisms allow the influenza virus to survive in humans, probably perpetually.

  3. Wild waterfowl migration and domestic duck density shape the epidemiology of highly pathogenic H5N8 influenza in the Republic of Korea

    PubMed Central

    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.

    2015-01-01

    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

  4. Wild waterfowl migration and domestic duck density shape the epidemiology of highly pathogenic H5N8 influenza in the Republic of Korea.

    PubMed

    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

    2015-08-01

    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.

  5. Real-Time Genomic Epidemiological Evaluation of Human Campylobacter Isolates by Use of Whole-Genome Multilocus Sequence Typing

    PubMed Central

    Cody, Alison J.; McCarthy, Noel D.; Jansen van Rensburg, Melissa; Isinkaye, Tomide; Bentley, Stephen D.; Parkhill, Julian; Dingle, Kate E.; Bowler, Ian C. J. W.; Jolley, Keith A.

    2013-01-01

    Sequence-based typing is essential for understanding the epidemiology of Campylobacter infections, a major worldwide cause of bacterial gastroenteritis. We demonstrate the practical and rapid exploitation of whole-genome sequencing to provide routine definitive characterization of Campylobacter jejuni and Campylobacter coli for clinical and public health purposes. Short-read data from 384 Campylobacter clinical isolates collected over 4 months in Oxford, United Kingdom, were assembled de novo. Contigs were deposited at the pubMLST.org/campylobacter website and automatically annotated for 1,667 loci. Typing and phylogenetic information was extracted and comparative analyses were performed for various subsets of loci, up to the level of the whole genome, using the Genome Comparator and Neighbor-net algorithms. The assembled sequences (for 379 isolates) were diverse and resembled collections from previous studies of human campylobacteriosis. Small subsets of very closely related isolates originated mainly from repeated sampling from the same patients and, in one case, likely laboratory contamination. Much of the within-patient variation occurred in phase-variable genes. Clinically and epidemiologically informative data can be extracted from whole-genome sequence data in real time with straightforward, publicly available tools. These analyses are highly scalable, are transparent, do not require closely related genome reference sequences, and provide improved resolution (i) among Campylobacter clonal complexes and (ii) between very closely related isolates. Additionally, these analyses rapidly differentiated unrelated isolates, allowing the detection of single-strain clusters. The approach is widely applicable to analyses of human bacterial pathogens in real time in clinical laboratories, with little specialist training required. PMID:23698529

  6. Isolation, propagation, genome analysis and epidemiology of HKU1 betacoronaviruses.

    PubMed

    Dominguez, Samuel R; Shrivastava, Susmita; Berglund, Andrew; Qian, Zhaohui; Góes, Luiz Gustavo Bentim; Halpin, Rebecca A; Fedorova, Nadia; Ransier, Amy; Weston, Philip A; Durigon, Edison Luiz; Jerez, José Antonio; Robinson, Christine C; Town, Christopher D; Holmes, Kathryn V

    2014-04-01

    From 1 January 2009 to 31 May 2013, 15 287 respiratory specimens submitted to the Clinical Virology Laboratory at the Children's Hospital Colorado were tested for human coronavirus RNA by reverse transcription-PCR. Human coronaviruses HKU1, OC43, 229E and NL63 co-circulated during each of the respiratory seasons but with significant year-to-year variability, and cumulatively accounted for 7.4-15.6 % of all samples tested during the months of peak activity. A total of 79 (0.5 % prevalence) specimens were positive for human betacoronavirus HKU1 RNA. Genotypes HKU1 A and B were both isolated from clinical specimens and propagated on primary human tracheal-bronchial epithelial cells cultured at the air-liquid interface and were neutralized in vitro by human intravenous immunoglobulin and by polyclonal rabbit antibodies to the spike glycoprotein of HKU1. Phylogenetic analysis of the deduced amino acid sequences of seven full-length genomes of Colorado HKU1 viruses and the spike glycoproteins from four additional HKU1 viruses from Colorado and three from Brazil demonstrated remarkable conservation of these sequences with genotypes circulating in Hong Kong and France. Within genotype A, all but one of the Colorado HKU1 sequences formed a unique subclade defined by three amino acid substitutions (W197F, F613Y and S752F) in the spike glycoprotein and exhibited a unique signature in the acidic tandem repeat in the N-terminal region of the nsp3 subdomain. Elucidating the function of and mechanisms responsible for the formation of these varying tandem repeats will increase our understanding of the replication process and pathogenicity of HKU1 and potentially of other coronaviruses.

  7. Genomic epidemiology and global diversity of the emerging bacterial pathogen Elizabethkingia anophelis

    PubMed Central

    Breurec, Sebastien; Criscuolo, Alexis; Diancourt, Laure; Rendueles, Olaya; Vandenbogaert, Mathias; Passet, Virginie; Caro, Valérie; Rocha, Eduardo P. C.; Touchon, Marie; Brisse, Sylvain

    2016-01-01

    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

  8. Genomic epidemiology and global diversity of the emerging bacterial pathogen Elizabethkingia anophelis.

    PubMed

    Breurec, Sebastien; Criscuolo, Alexis; Diancourt, Laure; Rendueles, Olaya; Vandenbogaert, Mathias; Passet, Virginie; Caro, Valérie; Rocha, Eduardo P C; Touchon, Marie; Brisse, Sylvain

    2016-01-01

    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

  9. Epidemiology and current status of allergic rhinitis, asthma, and associated allergic diseases in Korea: ARIA Asia-Pacific workshop report.

    PubMed

    Park, Hae Sim; Choi, Gil Soon; Cho, Joong Sang; Kim, You-Young

    2009-01-01

    The prevalence of allergic rhinitis and asthma has recently increased in Korea, and both conditions are recognized as major chronic respiratory diseases requiring active intervention. The prevalence of rhinitis among asthmatic patients is high, ranging from 60 to 80%, and could seriously affect asthma severity and outcome. We suggest that allergic rhinitis should be properly evaluated in asthmatic patients to achieve better asthma control.

  10. Neanderthal genomics suggests a pleistocene time frame for the first epidemiologic transition.

    PubMed

    Houldcroft, Charlotte J; Underdown, Simon J

    2016-07-01

    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. PMID:27063929

  11. Neanderthal genomics suggests a pleistocene time frame for the first epidemiologic transition.

    PubMed

    Houldcroft, Charlotte J; Underdown, Simon J

    2016-07-01

    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.

  12. Genomic epidemiology of age-associated meningococcal lineages in national surveillance: an observational cohort study

    PubMed Central

    Hill, Dorothea M C; Lucidarme, Jay; Gray, Stephen J; Newbold, Lynne S; Ure, Roisin; Brehony, Carina; Harrison, Odile B; Bray, James E; Jolley, Keith A; Bratcher, Holly B; Parkhill, Julian; Tang, Christoph M; Borrow, Ray; Maiden, Martin C J

    2015-01-01

    Summary Background Invasive meningococcal disease (IMD) is a worldwide health issue that is potentially preventable with vaccination. In view of its sporadic nature and the high diversity of Neisseria meningitidis, epidemiological surveillance incorporating detailed isolate characterisation is crucial for effective control and understanding the evolving epidemiology of IMD. The Meningitis Research Foundation Meningococcus Genome Library (MRF-MGL) exploits whole-genome sequencing (WGS) for this purpose and presents data on a comprehensive and coherent IMD isolate collection from England and Wales via the internet. We assessed the contribution of these data to investigating IMD epidemiology. Methods WGS data were obtained for all 899 IMD isolates available for England and Wales in epidemiological years 2010–11 and 2011–12. The data had been annotated at 1720 loci, analysed, and disseminated online. Information was also available on meningococcal population structure and vaccine (Bexsero, GlaxoSmithKline, Brentford, Middlesex, UK) antigen variants, which enabled the investigation of IMD-associated genotypes over time and by patients' age groups. Population genomic analyses were done with a hierarchical gene-by-gene approach. Findings The methods used by MRF-MGL efficiently characterised IMD isolates and information was provided in plain language. At least 20 meningococcal lineages were identified, three of which (hyperinvasive clonal complexes 41/44 [lineage 3], 269 [lineage 2], and 23 [lineage 23]) were responsible for 528 (59%) of IMD isolates. Lineages were highly diverse and showed evidence of extensive recombination. Specific lineages were associated with IMD in particular age groups, with notable diversity in the youngest and oldest individuals. The increased incidence of IMD from 1984 to 2010 in England and Wales was due to successive and concurrent epidemics of different lineages. Genetically, 74% of isolates were characterised as encoding group B capsules

  13. Characterization of a complete genome of a circular single-stranded DNA virus from porcine stools in Korea.

    PubMed

    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

    2014-02-01

    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.

  14. 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

    PubMed Central

    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

    2015-01-01

    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

  15. Genomics, evolution, and molecular epidemiology of the Streptococcus bovis/Streptococcus equinus complex (SBSEC).

    PubMed

    Jans, Christoph; Meile, Leo; Lacroix, Christophe; Stevens, Marc J A

    2015-07-01

    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

  16. Genomics, evolution, and molecular epidemiology of the Streptococcus bovis/Streptococcus equinus complex (SBSEC).

    PubMed

    Jans, Christoph; Meile, Leo; Lacroix, Christophe; Stevens, Marc J A

    2015-07-01

    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

  17. Acinetobacter seifertii Isolated from China: Genomic Sequence and Molecular Epidemiology Analyses.

    PubMed

    Yang, Yunxing; Wang, Jianfeng; Fu, Ying; Ruan, Zhi; Yu, Yunsong

    2016-03-01

    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. PMID

  18. Genomic Epidemiology: Whole-Genome-Sequencing-Powered Surveillance and Outbreak Investigation of Foodborne Bacterial Pathogens.

    PubMed

    Deng, Xiangyu; den Bakker, Henk C; Hendriksen, Rene S

    2016-01-01

    As we are approaching the twentieth anniversary of PulseNet, a network of public health and regulatory laboratories that has changed the landscape of foodborne illness surveillance through molecular subtyping, public health microbiology is undergoing another transformation brought about by so-called next-generation sequencing (NGS) technologies that have made whole-genome sequencing (WGS) of foodborne bacterial pathogens a realistic and superior alternative to traditional subtyping methods. Routine, real-time, and widespread application of WGS in food safety and public health is on the horizon. Technological, operational, and policy challenges are still present and being addressed by an international and multidisciplinary community of researchers, public health practitioners, and other stakeholders.

  19. Genomic Epidemiology: Whole-Genome-Sequencing-Powered Surveillance and Outbreak Investigation of Foodborne Bacterial Pathogens.

    PubMed

    Deng, Xiangyu; den Bakker, Henk C; Hendriksen, Rene S

    2016-01-01

    As we are approaching the twentieth anniversary of PulseNet, a network of public health and regulatory laboratories that has changed the landscape of foodborne illness surveillance through molecular subtyping, public health microbiology is undergoing another transformation brought about by so-called next-generation sequencing (NGS) technologies that have made whole-genome sequencing (WGS) of foodborne bacterial pathogens a realistic and superior alternative to traditional subtyping methods. Routine, real-time, and widespread application of WGS in food safety and public health is on the horizon. Technological, operational, and policy challenges are still present and being addressed by an international and multidisciplinary community of researchers, public health practitioners, and other stakeholders. PMID:26772415

  20. Complete mitochondrial genome of Upogebia yokoyai (Decapoda, Crustacea) from Jejudo, Korea.

    PubMed

    Yang, Eun Chan; Lee, Jimin; An, Sung Min; Choi, Dong Han; Noh, Jae Hoon

    2016-05-01

    The complete mitochondrial DNA of an ecologically important crustacean mud shrimp, Upogebia yokoyai (Decapoda, Crustacea) was sequenced. We used next generation sequencing strategy for total genomic DNA and organelle genome pipeline for mitogenome assembly. A newly determined mitogenome was 16,063 bp in total length with 28% of GC content. Thirty-seven genes were identified including 13 protein-coding genes, 2 rRNA genes, and 22 tRNA genes. We found ten case of overlapping between neighboring genes. Based on genome comparison, the mitogenome of U. yokoyai shows general crustacean gene content and identical synteny to the sister species, such as U. major and U. pusilla. Our results will provide useful information for mitochondrial genome diversity and evolution of the Crustacea.

  1. Clinical and epidemiological comparison of human metapneumovirus and respiratory syncytial virus in seoul, Korea, 2003-2008.

    PubMed

    Kim, Chang Keun; Choi, Jungi; Callaway, Zak; Kim, Hyo Bin; Chung, Ju Young; Koh, Young-Yull; Shin, Bo Moon

    2010-03-01

    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.

  2. Using whole-genome sequencing to determine appropriate streptomycin epidemiological cutoffs for Salmonella and Escherichia coli.

    PubMed

    Tyson, Gregory H; Li, Cong; Ayers, Sherry; McDermott, Patrick F; Zhao, Shaohua

    2016-02-01

    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.

  3. Complete Genome Sequence of a Canine-Origin H3N2 Feline Influenza Virus Isolated from Domestic Cats in South Korea.

    PubMed

    Park, Seong-Jun; Kang, Bo-Kyu; Jeoung, Hye-Young; Moon, Hyoung-Joon; Hong, Minki; Na, Woonseong; Park, Bong-Kyun; Poo, Haryoung; Kim, Jeong-Ki; An, Dong-Jun; Song, Dae-Sub

    2013-01-01

    A canine-origin Korean H3N2 feline influenza virus (FIV), A/feline/Korea/01/2010 (H3N2), was isolated in 2010 from a dead cat with severe respiratory disease. Here, we report the first complete genome sequence of this virus, containing 3' and 5' noncoding regions, which will help elucidate the molecular basis of the pathogenesis, transmission, and evolution of FIV.

  4. Complete genome sequence of an avian-origin H3N2 canine influenza virus isolated from dogs in South Korea.

    PubMed

    Park, Seong-Jun; Moon, Hyoung-Joon; Kang, Bo-Kyu; Hong, Minki; Na, Woonseong; Kim, Jeong-Ki; Poo, Haryoung; Park, Bong-Kyun; Song, Dae-Sub

    2012-09-01

    An avian-origin Korean H3N2 canine influenza virus (CIV) strain, designated A/canine/Korea/01/2007 (H3N2), was isolated from nasal swabs of pet dogs exhibiting severe respiratory syndrome in 2007. In the present study, we report the first complete genome sequence containing 3' and 5' noncoding regions (NCRs) of H3N2 CIV, which will provide important insights into the molecular basis of pathogenesis, transmission, and evolution of CIV.

  5. Identifying determinants of heterogeneous transmission dynamics of the Middle East respiratory syndrome (MERS) outbreak in the Republic of Korea, 2015: a retrospective epidemiological analysis

    PubMed Central

    Nishiura, Hiroshi; Endo, Akira; Saitoh, Masaya; Kinoshita, Ryo; Ueno, Ryo; Nakaoka, Shinji; Miyamatsu, Yuichiro; Dong, Yueping; Chowell, Gerardo; Mizumoto, Kenji

    2016-01-01

    Objectives To investigate the heterogeneous transmission patterns of Middle East respiratory syndrome (MERS) in the Republic of Korea, with a particular focus on epidemiological characteristics of superspreaders. Design Retrospective epidemiological analysis. Setting Multiple healthcare facilities of secondary and tertiary care centres in an urban setting. Participants A total of 185 laboratory-confirmed cases with partially known dates of illness onset and most likely sources of infection. Primary and secondary outcome measures Superspreaders were identified using the transmission tree. The reproduction number, that is, the average number of secondary cases produced by a single primary case, was estimated as a function of time and according to different types of hosts. Results A total of five superspreaders were identified. The reproduction number throughout the course of the outbreak was estimated at 1.0 due to reconstruction of the transmission tree, while the variance of secondary cases generated by a primary case was 52.1. All of the superspreaders involved in this outbreak appeared to have generated a substantial number of contacts in multiple healthcare facilities (association: p<0.01), generating on average 4.0 (0.0–8.6) and 28.6 (0.0–63.9) secondary cases among patients who visited multiple healthcare facilities and others. The time-dependent reproduction numbers declined substantially below the value of 1 on and after 13 June 2015. Conclusions Superspreaders who visited multiple facilities drove the epidemic by generating a disproportionate number of secondary cases. Our findings underscore the need to limit the contacts in healthcare settings. Contact tracing efforts could assist early laboratory testing and diagnosis of suspected cases. PMID:26908522

  6. The use of genomic DNA fingerprinting in studies of the epidemiology of bacteria in periodontitis.

    PubMed

    Genco, R J; Loos, B G

    1991-07-01

    Recent studies of microbial epidemiology emphasizing the genetic organization and distribution of organisms associated with orofacial infections have led to new insights into the possible origins of pathogenicity. Studies into genetic heterogeneity, acquisition and transmission of these organisms have been markedly advanced by the utilization of the powerful technique of genomic DNA fingerprinting. Characteristic fingerprints for each bacterial isolate can be produced by cleavage of high molecular weight genomic DNA by restriction endonucleases. It is assumed that each DNA fingerprint represents a clonal type. In this report, we review and analyze studies of the epidemiology of bacteria associated with orofacial infections with an emphasis on periodontal disease. Studies of nontypable (NT) Haemophilus influenzae associated with recurrent otitis media illustrate the utility of this technique. DNA fingerprinting clearly demonstrates genetic heterogeneity of NT H. influenzae isolates, and clonality of infection of any individual. Furthermore, DNA fingerprinting has shown that the same clonal type is seen in siblings concurrently suffering from otitis media, suggesting horizontal transmission within the family. Studies of mutans Streptococci also show extensive genetic heterogeneity and show vertical transmission of a predominant clonal type only from mother to infant, but not from father to infant. Studies of Actinobacillus actinomycetemcomitans show considerable genetic heterogeneity among monkey isolates. Thus far, three clonal types have been reported with DNA fingerprinting among isolates from periodontal patients, but additional genetic heterogeneity can be found using specific DNA fragments as probes in hybridization experiments. Intrafamilial transmission of A. actinomycetemcomitans has been demonstrated. Porphyromonas (Bacteroides) gingivalis shows extensive genetic heterogeneity and case reports suggest clonal infection of any one individual. In contrast

  7. Application of whole-genome sequencing for bacterial strain typing in molecular epidemiology.

    PubMed

    Salipante, Stephen J; SenGupta, Dhruba J; Cummings, Lisa A; Land, Tyler A; Hoogestraat, Daniel R; Cookson, Brad T

    2015-04-01

    Nosocomial infections pose a significant threat to patient health; however, the gold standard laboratory method for determining bacterial relatedness (pulsed-field gel electrophoresis [PFGE]) remains essentially unchanged 20 years after its introduction. Here, we explored bacterial whole-genome sequencing (WGS) as an alternative approach for molecular strain typing. We compared WGS to PFGE for investigating presumptive outbreaks involving three important pathogens: vancomycin-resistant Enterococcus faecium (n=19), methicillin-resistant Staphylococcus aureus (n=17), and Acinetobacter baumannii (n=15). WGS was highly reproducible (average≤0.39 differences between technical replicates), which enabled a functional, quantitative definition for determining clonality. Strain relatedness data determined by PFGE and WGS roughly correlated, but the resolution of WGS was superior (P=5.6×10(-8) to 0.016). Several discordant results were noted between the methods. A total of 28.9% of isolates which were indistinguishable by PFGE were nonclonal by WGS. For A. baumannii, a species known to undergo rapid horizontal gene transfer, 16.2% of isolate pairs considered nonidentical by PFGE were clonal by WGS. Sequencing whole bacterial genomes with single-nucleotide resolution demonstrates that PFGE is prone to false-positive and false-negative results and suggests the need for a new gold standard approach for molecular epidemiological strain typing.

  8. Application of whole-genome sequencing for bacterial strain typing in molecular epidemiology.

    PubMed

    Salipante, Stephen J; SenGupta, Dhruba J; Cummings, Lisa A; Land, Tyler A; Hoogestraat, Daniel R; Cookson, Brad T

    2015-04-01

    Nosocomial infections pose a significant threat to patient health; however, the gold standard laboratory method for determining bacterial relatedness (pulsed-field gel electrophoresis [PFGE]) remains essentially unchanged 20 years after its introduction. Here, we explored bacterial whole-genome sequencing (WGS) as an alternative approach for molecular strain typing. We compared WGS to PFGE for investigating presumptive outbreaks involving three important pathogens: vancomycin-resistant Enterococcus faecium (n=19), methicillin-resistant Staphylococcus aureus (n=17), and Acinetobacter baumannii (n=15). WGS was highly reproducible (average≤0.39 differences between technical replicates), which enabled a functional, quantitative definition for determining clonality. Strain relatedness data determined by PFGE and WGS roughly correlated, but the resolution of WGS was superior (P=5.6×10(-8) to 0.016). Several discordant results were noted between the methods. A total of 28.9% of isolates which were indistinguishable by PFGE were nonclonal by WGS. For A. baumannii, a species known to undergo rapid horizontal gene transfer, 16.2% of isolate pairs considered nonidentical by PFGE were clonal by WGS. Sequencing whole bacterial genomes with single-nucleotide resolution demonstrates that PFGE is prone to false-positive and false-negative results and suggests the need for a new gold standard approach for molecular epidemiological strain typing. PMID:25631811

  9. Epidemiology.

    PubMed

    Walsh, Kyle M; Ohgaki, Hiroko; Wrensch, Margaret R

    2016-01-01

    More than 250,000 new cases of primary malignant brain tumors are diagnosed annually worldwide, 77% of which are gliomas. A small proportion of gliomas are caused by the inheritance of rare high-penetrance genetic variants or high-dose radiation. Since 2009, inherited genetic variants in 10 regions near eight different genes have been consistently associated with glioma risk via genome-wide association studies. Most of these variants increase glioma risk by 20-40%, but two have higher relative risks. One on chromosome 8 increases risk of IDH-mutated gliomas sixfold and another that affects TP53 function confers a 2.5-fold increased risk of glioma. Functions of some of the other risk variants are known or suspected, but future research will determine functions of other risk loci. Recent progress also has been made in defining subgroups of glioma based on acquired alterations within tumors. Allergy history has been consistently associated with reduced glioma risk, though the mechanisms have not yet been clarified. Future studies will need to be large enough so that environmental and constitutive genetic risk factors can be examined within molecularly defined, etiologically homogeneous subgroups.

  10. Genome-wide Mycobacterium tuberculosis variation (GMTV) database: a new tool for integrating sequence variations and epidemiology

    PubMed Central

    2014-01-01

    Background Tuberculosis (TB) poses a worldwide threat due to advancing multidrug-resistant strains and deadly co-infections with Human immunodeficiency virus. Today large amounts of Mycobacterium tuberculosis whole genome sequencing data are being assessed broadly and yet there exists no comprehensive online resource that connects M. tuberculosis genome variants with geographic origin, with drug resistance or with clinical outcome. Description Here we describe a broadly inclusive unifying Genome-wide Mycobacterium tuberculosis Variation (GMTV) database, (http://mtb.dobzhanskycenter.org) that catalogues genome variations of M. tuberculosis strains collected across Russia. GMTV contains a broad spectrum of data derived from different sources and related to M. tuberculosis molecular biology, epidemiology, TB clinical outcome, year and place of isolation, drug resistance profiles and displays the variants across the genome using a dedicated genome browser. GMTV database, which includes 1084 genomes and over 69,000 SNP or Indel variants, can be queried about M. tuberculosis genome variation and putative associations with drug resistance, geographical origin, and clinical stages and outcomes. Conclusions Implementation of GMTV tracks the pattern of changes of M. tuberculosis strains in different geographical areas, facilitates disease gene discoveries associated with drug resistance or different clinical sequelae, and automates comparative genomic analyses among M. tuberculosis strains. PMID:24767249

  11. Epidemiological and Genomic Landscape of Azole Resistance Mechanisms in Aspergillus Fungi

    PubMed Central

    Hagiwara, Daisuke; Watanabe, Akira; Kamei, Katsuhiko; Goldman, Gustavo H.

    2016-01-01

    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

  12. Genomic Epidemiology of Methicillin-Resistant Staphylococcus aureus in a Neonatal Intensive Care Unit

    PubMed Central

    Maraqa, Nizar F.; Cook, Robert L.; Johnson, Judith A.; Bailey, Christine; Wheeler, Sarah; Nolan, David; Rathore, Mobeen H.; Morris, J. Glenn; Salemi, Marco

    2016-01-01

    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

  13. Utility of Whole-Genome Sequencing in Characterizing Acinetobacter Epidemiology and Analyzing Hospital Outbreaks

    PubMed Central

    Fitzpatrick, Margaret A.; Hauser, Alan R.

    2015-01-01

    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

  14. Data sharing and intellectual property in a genomic epidemiology network: policies for large-scale research collaboration.

    PubMed Central

    Chokshi, Dave A.; Parker, Michael; Kwiatkowski, Dominic P.

    2006-01-01

    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

  15. Epidemiologic features of the first MERS outbreak in Korea: focus on Pyeongtaek St. Mary’s Hospital

    PubMed Central

    Kim, Kyung Min; Ki, Moran; Cho, Sung-il; Sung, Minki; Hong, Jin Kwan; Cheong, Hae-Kwan; Kim, Jong-Hun; Lee, Sang-Eun; Lee, Changhwan; Lee, Keon-Joo; Park, Yong-Shik; Kim, Seung Woo; Choi, Bo Youl

    2015-01-01

    OBJECTIVES: This study investigated the epidemiologic features of the confirmed cases of Middle East Respiratory Syndrome (MERS) in Pyeongtaek St. Mary’s Hospital, where the outbreak first began, in order to identify lessons relevant for the prevention and control of future outbreaks. METHODS: The patients’ clinical symptoms and test results were collected from their medical records. The caregivers of patients were identified by phone calls. RESULTS: After patient zero (case #1) was admitted to Pyeongtaek St. Mary’s Hospital (May 15-May 17), an outbreak occurred, with 36 cases between May 18 and June 4, 2015. Six patients died (fatality rate, 16.7%). Twenty-six cases occurred in the first-generation, and 10 in the second-generation. The median incubation period was five days, while the median period from symptom onset to death was 12.5 days. While the total attack rate was 3.9%, the attack rate among inpatients was 7.6%, and the inpatients on the eighth floor, where patient zero was hospitalized, had an 18.6% attack rate. In contrast, caregivers and medical staff showed attack rates of 3.3% and 1.1%, respectively. CONCLUSIONS: The attack rates were higher than those of the previous outbreaks in other countries. The outbreak spread beyond Pyeongtaek St. Mary’s Hospital when four of the patients were moved to other hospitals without appropriate quarantine. The best method of preventing future outbreaks is to overcome the vulnerabilities observed in this outbreak, such as ward crowding, patient migration without appropriate data sharing, and the lack of an initial broad quarantine. PMID:26725225

  16. Complete genome sequence of Deinococcus soli N5(T), a gamma-radiation- resistant bacterium isolated from rice field in South Korea.

    PubMed

    Joo, Eun Sun; Kim, Eun Bit; Jeon, Seon Hwa; Srinivasan, Sathiyaraj

    2015-10-10

    A Gram-negative, non-motile and short-rod shaped and gamma-radiation-resistant bacterium Deinococcus soli N5(T), isolated from a rice field soil in South Korea. The complete genome of D. soli N5(T) consists of a chromosome (3,236,984bp). The key enzymes for the central DNA repair mechanisms were present in the genome. The enzyme coding genes has been identified which is involving in the nucleotide excision repair (NER) pathway. The gene cluster in the genome sequence suggest that the D. soli N5(T) use (NER) pathways for efficient removal of pyrimidine dimers that are the most abundant type of UV- induced damage.

  17. Kvik: three-tier data exploration tools for flexible analysis of genomic data in epidemiological studies

    PubMed Central

    Fjukstad, Bjørn; Standahl Olsen, Karina; Jareid, Mie; Lund, Eiliv; Bongo, Lars Ailo

    2015-01-01

    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

  18. Kvik: three-tier data exploration tools for flexible analysis of genomic data in epidemiological studies.

    PubMed

    Fjukstad, Bjørn; Standahl Olsen, Karina; Jareid, Mie; Lund, Eiliv; Bongo, Lars Ailo

    2015-01-01

    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

  19. Kvik: three-tier data exploration tools for flexible analysis of genomic data in epidemiological studies.

    PubMed

    Fjukstad, Bjørn; Standahl Olsen, Karina; Jareid, Mie; Lund, Eiliv; Bongo, Lars Ailo

    2015-01-01

    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.

  20. Complete genome sequence of a natural reassortant H9N2 avian influenza virus found in bean goose (Anser fabalis): direct evidence for virus exchange between Korea and China via wild birds.

    PubMed

    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

    2014-08-01

    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.

  1. Brief report: genome sequence and construction of an infectious cDNA clone of Ribgrass mosaic virus from Chinese cabbage in Korea.

    PubMed

    Ryu, So-Young; Hong, Jin-Sung; Rhee, Sun-Ju; Lee, Gung Pyo

    2012-04-01

    Ribgrass mosaic virus (RMV) has severely decreased the production and lowered quality of Chinese cabbage co-infected with Turnip mosaic virus (63.4%) in Korea. The complete genome sequence of RMV isolated from Brassica rapa ssp. pekinensis was determined. The full genome consisted of 6,304 nucleotides and showed sequence identities of 91.5-94.2% with the corresponding genome of other RMV strains. Full-length cDNA of RMV-Br was amplified by RT-PCR with a 5'-end primer harboring a T7 promoter sequence and a 3'-end RMV specific primer. Subsequently, the full-length cDNA was cloned into plasmid vectors. Capped transcripts synthesized from the cDNA clone were highly infectious and caused characteristic symptoms in B. rapa ssp. pekinensis and several indicator plants, similar to wild type RMV. Since there has not been found RMV resistant Chinese cabbage yet and the virus has been prevalent already throughout the natural fields of Korea, the identification of full sequence and development of infectious clone would help developing breeding program for RMV resistant crops.

  2. Brief report: genome sequence and construction of an infectious cDNA clone of Ribgrass mosaic virus from Chinese cabbage in Korea.

    PubMed

    Ryu, So-Young; Hong, Jin-Sung; Rhee, Sun-Ju; Lee, Gung Pyo

    2012-04-01

    Ribgrass mosaic virus (RMV) has severely decreased the production and lowered quality of Chinese cabbage co-infected with Turnip mosaic virus (63.4%) in Korea. The complete genome sequence of RMV isolated from Brassica rapa ssp. pekinensis was determined. The full genome consisted of 6,304 nucleotides and showed sequence identities of 91.5-94.2% with the corresponding genome of other RMV strains. Full-length cDNA of RMV-Br was amplified by RT-PCR with a 5'-end primer harboring a T7 promoter sequence and a 3'-end RMV specific primer. Subsequently, the full-length cDNA was cloned into plasmid vectors. Capped transcripts synthesized from the cDNA clone were highly infectious and caused characteristic symptoms in B. rapa ssp. pekinensis and several indicator plants, similar to wild type RMV. Since there has not been found RMV resistant Chinese cabbage yet and the virus has been prevalent already throughout the natural fields of Korea, the identification of full sequence and development of infectious clone would help developing breeding program for RMV resistant crops. PMID:22143325

  3. Genomic Epidemiology of an Endoscope-Associated Outbreak of Klebsiella pneumoniae Carbapenemase (KPC)-Producing K. pneumoniae

    PubMed Central

    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.

    2015-01-01

    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

  4. Genomic Epidemiology of an Endoscope-Associated Outbreak of Klebsiella pneumoniae Carbapenemase (KPC)-Producing K. pneumoniae.

    PubMed

    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

    2015-01-01

    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

  5. Utility of Whole-Genome Sequencing of Escherichia coli O157 for Outbreak Detection and Epidemiological Surveillance

    PubMed Central

    Allison, Lesley; Ward, Melissa; Dallman, Timothy J.; Clark, Richard; Fawkes, Angie; Murphy, Lee; Hanson, Mary

    2015-01-01

    Detailed laboratory characterization of Escherichia coli O157 is essential to inform epidemiological investigations. This study assessed the utility of whole-genome sequencing (WGS) for outbreak detection and epidemiological surveillance of E. coli O157, and the data were used to identify discernible associations between genotypes and clinical outcomes. One hundred five E. coli O157 strains isolated over a 5-year period from human fecal samples in Lothian, Scotland, were sequenced with the Ion Torrent Personal Genome Machine. A total of 8,721 variable sites in the core genome were identified among the 105 isolates; 47% of the single nucleotide polymorphisms (SNPs) were attributable to six “atypical” E. coli O157 strains and included recombinant regions. Phylogenetic analyses showed that WGS correlated well with the epidemiological data. Epidemiological links existed between cases whose isolates differed by three or fewer SNPs. WGS also correlated well with multilocus variable-number tandem repeat analysis (MLVA) typing data, with only three discordant results observed, all among isolates from cases not known to be epidemiologically related. WGS produced a better-supported, higher-resolution phylogeny than MLVA, confirming that the method is more suitable for epidemiological surveillance of E. coli O157. A combination of in silico analyses (VirulenceFinder, ResFinder, and local BLAST searches) were used to determine stx subtypes, multilocus sequence types (15 loci), and the presence of virulence and acquired antimicrobial resistance genes. There was a high level of correlation between the WGS data and our routine typing methods, although some discordant results were observed, mostly related to the limitation of short sequence read assembly. The data were used to identify sublineages and clades of E. coli O157, and when they were correlated with the clinical outcome data, they showed that one clade, Ic3, was significantly associated with severe disease. Together

  6. Utility of Whole-Genome Sequencing of Escherichia coli O157 for Outbreak Detection and Epidemiological Surveillance.

    PubMed

    Holmes, Anne; Allison, Lesley; Ward, Melissa; Dallman, Timothy J; Clark, Richard; Fawkes, Angie; Murphy, Lee; Hanson, Mary

    2015-11-01

    Detailed laboratory characterization of Escherichia coli O157 is essential to inform epidemiological investigations. This study assessed the utility of whole-genome sequencing (WGS) for outbreak detection and epidemiological surveillance of E. coli O157, and the data were used to identify discernible associations between genotypes and clinical outcomes. One hundred five E. coli O157 strains isolated over a 5-year period from human fecal samples in Lothian, Scotland, were sequenced with the Ion Torrent Personal Genome Machine. A total of 8,721 variable sites in the core genome were identified among the 105 isolates; 47% of the single nucleotide polymorphisms (SNPs) were attributable to six "atypical" E. coli O157 strains and included recombinant regions. Phylogenetic analyses showed that WGS correlated well with the epidemiological data. Epidemiological links existed between cases whose isolates differed by three or fewer SNPs. WGS also correlated well with multilocus variable-number tandem repeat analysis (MLVA) typing data, with only three discordant results observed, all among isolates from cases not known to be epidemiologically related. WGS produced a better-supported, higher-resolution phylogeny than MLVA, confirming that the method is more suitable for epidemiological surveillance of E. coli O157. A combination of in silico analyses (VirulenceFinder, ResFinder, and local BLAST searches) were used to determine stx subtypes, multilocus sequence types (15 loci), and the presence of virulence and acquired antimicrobial resistance genes. There was a high level of correlation between the WGS data and our routine typing methods, although some discordant results were observed, mostly related to the limitation of short sequence read assembly. The data were used to identify sublineages and clades of E. coli O157, and when they were correlated with the clinical outcome data, they showed that one clade, Ic3, was significantly associated with severe disease. Together, the

  7. Comparison of whole genome sequencing typing results and epidemiological contact information from outbreaks of Salmonella Dublin in Swedish cattle herds

    PubMed Central

    Ågren, Estelle C. C.; Wahlström, Helene; Vesterlund-Carlson, Catrin; Lahti, Elina; Melin, Lennart; Söderlund, Robert

    2016-01-01

    Background Whole genome sequencing (WGS) is becoming a routine tool for infectious disease outbreak investigations. The Swedish situation provides an excellent opportunity to test the usefulness of WGS for investigation of outbreaks with Salmonella Dublin (S. Dublin) as epidemiological investigations are always performed when Salmonella is detected in livestock production, and index isolates from all detected herds are stored and therefore available for analysis. This study was performed to evaluate WGS as a tool in forward and backward tracings from herds infected with S. Dublin. Material and methods In this study, 28 isolates from 26 cattle herds were analysed and the WGS results were compared with results from the epidemiological investigations, for example, information on contacts between herds. The isolates originated from herds in three different outbreaks separated geographically and to some extent also in time, and from the only region in Sweden where S. Dublin is endemic (Öland). Results The WGS results of isolates from the three non-endemic regions were reliably separated from each other and from the endemic isolates. Within the outbreaks, herds with known epidemiological contacts generally showed smaller differences between isolates as compared to when there were no known epidemiological contacts. Conclusion The results indicate that WGS can provide valuable supplemental information in S. Dublin outbreak investigations. The resolution of the WGS was sufficient to distinguish isolates from the different outbreaks and provided additional information to the investigations within an outbreak. PMID:27396609

  8. Whole Genome Sequencing versus Traditional Genotyping for Investigation of a Mycobacterium tuberculosis Outbreak: A Longitudinal Molecular Epidemiological Study

    PubMed Central

    Rückert, Christian; Nübel, Ulrich; Blom, Jochen; Wirth, Thierry; Jaenicke, Sebastian; Schuback, Sieglinde; Rüsch-Gerdes, Sabine; Supply, Philip; Kalinowski, Jörn; Niemann, Stefan

    2013-01-01

    Background Understanding Mycobacterium tuberculosis (Mtb) transmission is essential to guide efficient tuberculosis control strategies. Traditional strain typing lacks sufficient discriminatory power to resolve large outbreaks. Here, we tested the potential of using next generation genome sequencing for identification of outbreak-related transmission chains. Methods and Findings During long-term (1997 to 2010) prospective population-based molecular epidemiological surveillance comprising a total of 2,301 patients, we identified a large outbreak caused by an Mtb strain of the Haarlem lineage. The main performance outcome measure of whole genome sequencing (WGS) analyses was the degree of correlation of the WGS analyses with contact tracing data and the spatio-temporal distribution of the outbreak cases. WGS analyses of the 86 isolates revealed 85 single nucleotide polymorphisms (SNPs), subdividing the outbreak into seven genome clusters (two to 24 isolates each), plus 36 unique SNP profiles. WGS results showed that the first outbreak isolates detected in 1997 were falsely clustered by classical genotyping. In 1998, one clone (termed “Hamburg clone”) started expanding, apparently independently from differences in the social environment of early cases. Genome-based clustering patterns were in better accordance with contact tracing data and the geographical distribution of the cases than clustering patterns based on classical genotyping. A maximum of three SNPs were identified in eight confirmed human-to-human transmission chains, involving 31 patients. We estimated the Mtb genome evolutionary rate at 0.4 mutations per genome per year. This rate suggests that Mtb grows in its natural host with a doubling time of approximately 22 h (400 generations per year). Based on the genome variation discovered, emergence of the Hamburg clone was dated back to a period between 1993 and 1997, hence shortly before the discovery of the outbreak through epidemiological surveillance

  9. Integration of Genomic and Other Epidemiologic Data to Investigate and Control a Cross-Institutional Outbreak of Streptococcus pyogenes

    PubMed Central

    Chalker, Victoria J.; Smith, Alyson; Al-Shahib, Ali; Botchway, Stella; Macdonald, Emily; Daniel, Roger; Phillips, Sarah; Platt, Steven; Doumith, Michel; Tewolde, Rediat; Coelho, Juliana; Jolley, Keith A.; Underwood, Anthony

    2016-01-01

    Single-strain outbreaks of Streptococcus pyogenes infections are common and often go undetected. In 2013, two clusters of invasive group A Streptococcus (iGAS) infection were identified in independent but closely located care homes in Oxfordshire, United Kingdom. Investigation included visits to each home, chart review, staff survey, microbiologic sampling, and genome sequencing. S. pyogenes emm type 1.0, the most common circulating type nationally, was identified from all cases yielding GAS isolates. A tailored whole-genome reference population comprising epidemiologically relevant contemporaneous isolates and published isolates was assembled. Data were analyzed independently using whole-genome multilocus sequencing and single-nucleotide polymorphism analyses. Six isolates from staff and residents of the homes formed a single cluster that was separated from the reference population by both analytical approaches. No further cases occurred after mass chemoprophylaxis and enhanced infection control. Our findings demonstrate the ability of 2 independent analytical approaches to enable robust conclusions from nonstandardized whole-genome analysis to support public health practice. PMID:27192043

  10. Aspects of pathogen genomics, diversity, epidemiology, vector dynamics, and disease management for a newly emerged disease of potato: zebra chip.

    PubMed

    Lin, Hong; Gudmestad, Neil C

    2013-06-01

    An overview is provided for the aspects of history, biology, genomics, genetics, and epidemiology of zebra chip (ZC), a destructive disease of potato (Solanum tuberosum) that represents a major threat to the potato industries in the United States as well as other potato-production regions in the world. The disease is associated with a gram-negative, phloem-limited, insect-vectored, unculturable prokaryote, 'Candidatus Liberibacter solanacearum', that belongs to the Rhizobiaceae family of α-Proteobacteria. The closest cultivated relatives of 'Ca. L. solanacearum' are members of the group of bacteria known as the α-2 subgroup. In spite of the fact that Koch's postulates sensu stricto have not been fulfilled, a great deal of progress has been made in understanding the ZC disease complex since discovery of the disease. Nevertheless, more research is needed to better understand vector biology, disease mechanisms, host response, and epidemiology in the context of vector-pathogen-plant interactions. Current ZC management strategies focus primarily on psyllid control. The ultimate control of ZC likely relies on host resistance. Unfortunately, all commercial potato cultivars are susceptible to ZC. Elucidation of the 'Ca. L. solanacearum' genome sequence has provided insights into the genetic basis of virulence and physiological and metabolic capability of this organism. Finally, the most effective, sustainable management of ZC is likely to be based on integrated strategies, including removal or reduction of vectors or inocula, improvement of host resistance to the presumptive pathogen and psyllid vectors, and novel gene-based therapeutic treatment.

  11. Cancer Epidemiology Matters Blog

    Cancer.gov

    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.

  12. A large-scale genomic approach affords unprecedented resolution for the molecular epidemiology and evolutionary history of contagious caprine pleuropneumonia.

    PubMed

    Dupuy, Virginie; Verdier, Axel; Thiaucourt, François; Manso-Silván, Lucía

    2015-01-01

    Contagious caprine pleuropneumonia (CCPP), caused by Mycoplasma capricolum subsp. capripneumoniae (Mccp), is a devastating disease of domestic goats and of some wild ungulate species. The disease is currently spreading in Africa and Asia and poses a serious threat to disease-free areas. A comprehensive view of the evolutionary history and dynamics of Mccp is essential to understand the epidemiology of CCPP. Yet, analysing the diversity of genetically monomorphic pathogens, such as Mccp, is complicated due to their low variability. In this study, the molecular epidemiology and evolution of CCPP was investigated using a large-scale genomic approach based on next-generation sequencing technologies, applied to a sample of strains representing the global distribution of this disease. A highly discriminatory multigene typing system was developed, allowing the differentiation of 24 haplotypes among 25 Mccp strains distributed in six genotyping groups, which showed some correlation with geographic origin. A Bayesian approach was used to infer the first robust phylogeny of the species and to date the principal events of its evolutionary history. The emergence of Mccp was estimated only at about 270 years ago, which explains the low genetic diversity of this species despite its high mutation rate, evaluated at 1.3 × 10(-6) substitutions per site per year. Finally, plausible scenarios were proposed to elucidate the evolution and dynamics of CCPP in Asia and Africa, though limited by the paucity of Mccp strains, particularly in Asia. This study shows how combining large-scale genomic data with spatial and temporal data makes it possible to obtain a comprehensive view of the epidemiology of CCPP, a precondition for the development of improved disease surveillance and control measures. PMID:26149260

  13. Genomic Epidemiology and Molecular Resistance Mechanisms of Azithromycin-Resistant Neisseria gonorrhoeae in Canada from 1997 to 2014.

    PubMed

    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; Mulvey, Michael R

    2016-05-01

    The emergence of Neisseria gonorrhoeae strains with decreased susceptibility to cephalosporins and azithromycin (AZM) resistance (AZM(r)) 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 AZM(r) strains. The genomes of 213 AZM(r) 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 AZM(r) (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 AZM(r) 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 AZM(r) (MICs = 2 to 4 and 8 to 32 μg/ml, respectively). Low-level AZM(r) 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 AZM(r) strains arise independently and can then rapidly expand clonally in a region through local sexual networks. PMID:26935729

  14. Ethical issues in human genome epidemiology: a case study based on the Japanese American Family Study in Seattle, Washington.

    PubMed

    Austin, Melissa A

    2002-04-01

    Recent completion of the draft sequence of the human genome has been greeted with both excitement and skepticism, and the potential of this accomplishment for advancing public health has been tempered by ethical concerns about the protection of human subjects. This commentary explores ethical issues arising in human genome epidemiology by using a case study approach based on the ongoing Japanese American Family Study at the University of Washington in Seattle (1994-2003). Ethical issues encountered in designing the study, collecting the data, and reporting the study results are considered. When developing studies, investigators must consider whether to restrict the study to specific racial or ethnic groups and whether community involvement is appropriate. Once the study design is in place, further ethical issues emerge, including obtaining informed consent for DNA banking and protecting the privacy and confidentiality of family members. Finally, investigators must carefully consider whether to report genotype results to study participants and whether pedigrees illustrating the results of the study will be published. Overall, the promise of genomics for improving public health must be pursued based on the fundamental ethical principles of respect for persons, beneficence, and justice.

  15. Genome-wide Studies of Verbal Declarative Memory in Nondemented Older People: The Cohorts for Heart and Aging Research in Genomic Epidemiology Consortium

    PubMed Central

    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.

    2015-01-01

    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

  16. A genome-wide association study for venous thromboembolism: the extended cohorts for heart and aging research in genomic epidemiology (CHARGE) consortium.

    PubMed

    Tang, Weihong; Teichert, Martina; Chasman, Daniel I; Heit, John A; Morange, Pierre-Emmanuel; Li, Guo; Pankratz, Nathan; Leebeek, Frank W; Paré, Guillaume; de Andrade, Mariza; Tzourio, Christophe; Psaty, Bruce M; Basu, Saonli; Ruiter, Rikje; Rose, Lynda; Armasu, Sebastian M; Lumley, Thomas; Heckbert, Susan R; Uitterlinden, André G; Lathrop, Mark; Rice, Kenneth M; Cushman, Mary; Hofman, Albert; Lambert, Jean-Charles; Glazer, Nicole L; Pankow, James S; Witteman, Jacqueline C; Amouyel, Philippe; Bis, Joshua C; Bovill, Edwin G; Kong, Xiaoxiao; Tracy, Russell P; Boerwinkle, Eric; Rotter, Jerome I; Trégouët, David-Alexandre; Loth, Daan W; Stricker, Bruno H Ch; Ridker, Paul M; Folsom, Aaron R; Smith, Nicholas L

    2013-07-01

    Venous thromboembolism (VTE) is a common, heritable disease resulting in high rates of hospitalization and mortality. Yet few associations between VTE and genetic variants, all in the coagulation pathway, have been established. To identify additional genetic determinants of VTE, we conducted a two-stage genome-wide association study (GWAS) among individuals of European ancestry in the extended cohorts for heart and aging research in genomic epidemiology (CHARGE) VTE consortium. The discovery GWAS comprised 1,618 incident VTE cases out of 44,499 participants from six community-based studies. Genotypes for genome-wide single-nucleotide polymorphisms (SNPs) were imputed to approximately 2.5 million SNPs in HapMap and association with VTE assessed using study-design appropriate regression methods. Meta-analysis of these results identified two known loci, in F5 and ABO. Top 1,047 tag SNPs (P ≤ 0.0016) from the discovery GWAS were tested for association in an additional 3,231 cases and 3,536 controls from three case-control studies. In the combined data from these two stages, additional genome-wide significant associations were observed on 4q35 at F11 (top SNP rs4253399, intronic to F11) and on 4q28 at FGG (rs6536024, 9.7 kb from FGG; P < 5.0 × 10(-13) for both). The associations at the FGG locus were not completely explained by previously reported variants. Loci at or near SUSD1 and OTUD7A showed borderline yet novel associations (P < 5.0 × 10(-6) ) and constitute new candidate genes. In conclusion, this large GWAS replicated key genetic associations in F5 and ABO, and confirmed the importance of F11 and FGG loci for VTE. Future studies are warranted to better characterize the associations with F11 and FGG and to replicate the new candidate associations.

  17. [South] Korea.

    PubMed

    1987-04-01

    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

  18. [South] Korea.

    PubMed

    1987-04-01

    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

  19. Role of Genomic Typing in Taxonomy, Evolutionary Genetics, and Microbial Epidemiology

    PubMed Central

    van Belkum, Alex; Struelens, Marc; de Visser, Arjan; Verbrugh, Henri; Tibayrenc, Michel

    2001-01-01

    Currently, genetic typing of microorganisms is widely used in several major fields of microbiological research. Taxonomy, research aimed at elucidation of evolutionary dynamics or phylogenetic relationships, population genetics of microorganisms, and microbial epidemiology all rely on genetic typing data for discrimination between genotypes. Apart from being an essential component of these fundamental sciences, microbial typing clearly affects several areas of applied microbiogical research. The epidemiological investigation of outbreaks of infectious diseases and the measurement of genetic diversity in relation to relevant biological properties such as pathogenicity, drug resistance, and biodegradation capacities are obvious examples. The diversity among nucleic acid molecules provides the basic information for all fields described above. However, researchers in various disciplines tend to use different vocabularies, a wide variety of different experimental methods to monitor genetic variation, and sometimes widely differing modes of data processing and interpretation. The aim of the present review is to summarize the technological and fundamental concepts used in microbial taxonomy, evolutionary genetics, and epidemiology. Information on the nomenclature used in the different fields of research is provided, descriptions of the diverse genetic typing procedures are presented, and examples of both conceptual and technological research developments for Escherichia coli are included. Recommendations for unification of the different fields through standardization of laboratory techniques are made. PMID:11432813

  20. Integrated Bioinformatics, Environmental Epidemiologic and Genomic Approaches to Identify Environmental and Molecular Links between Endometriosis and Breast Cancer

    PubMed Central

    Roy, Deodutta; Morgan, Marisa; Yoo, Changwon; Deoraj, Alok; Roy, Sandhya; Yadav, Vijay Kumar; Garoub, Mohannad; Assaggaf, Hamza; Doke, Mayur

    2015-01-01

    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

  1. Integrated Bioinformatics, Environmental Epidemiologic and Genomic Approaches to Identify Environmental and Molecular Links between Endometriosis and Breast Cancer.

    PubMed

    Roy, Deodutta; Morgan, Marisa; Yoo, Changwon; Deoraj, Alok; Roy, Sandhya; Yadav, Vijay Kumar; Garoub, Mohannad; Assaggaf, Hamza; Doke, Mayur

    2015-01-01

    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

  2. Integrated Bioinformatics, Environmental Epidemiologic and Genomic Approaches to Identify Environmental and Molecular Links between Endometriosis and Breast Cancer.

    PubMed

    Roy, Deodutta; Morgan, Marisa; Yoo, Changwon; Deoraj, Alok; Roy, Sandhya; Yadav, Vijay Kumar; Garoub, Mohannad; Assaggaf, Hamza; Doke, Mayur

    2015-10-23

    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.

  3. Full-Genome Sequencing as a Basis for Molecular Epidemiology Studies of Bluetongue Virus in India.

    PubMed

    Maan, Sushila; Maan, Narender S; Belaganahalli, Manjunatha N; Rao, Pavuluri Panduranga; Singh, Karam Pal; Hemadri, Divakar; Putty, Kalyani; Kumar, Aman; Batra, Kanisht; Krishnajyothi, Yadlapati; Chandel, Bharat S; Reddy, G Hanmanth; Nomikou, Kyriaki; Reddy, Yella Narasimha; Attoui, Houssam; Hegde, Nagendra R; Mertens, Peter P C

    2015-01-01

    Since 1998 there have been significant changes in the global distribution of bluetongue virus (BTV). Ten previously exotic BTV serotypes have been detected in Europe, causing severe disease outbreaks in naïve ruminant populations. Previously exotic BTV serotypes were also identified in the USA, Israel, Australia and India. BTV is transmitted by biting midges (Culicoides spp.) and changes in the distribution of vector species, climate change, increased international travel and trade are thought to have contributed to these events. Thirteen BTV serotypes have been isolated in India since first reports of the disease in the country during 1964. Efficient methods for preparation of viral dsRNA and cDNA synthesis, have facilitated full-genome sequencing of BTV strains from the region. These studies introduce a new approach for BTV characterization, based on full-genome sequencing and phylogenetic analyses, facilitating the identification of BTV serotype, topotype and reassortant strains. Phylogenetic analyses show that most of the equivalent genome-segments of Indian BTV strains are closely related, clustering within a major eastern BTV 'topotype'. However, genome-segment 5 (Seg-5) encoding NS1, from multiple post 1982 Indian isolates, originated from a western BTV topotype. All ten genome-segments of BTV-2 isolates (IND2003/01, IND2003/02 and IND2003/03) are closely related (>99% identity) to a South African BTV-2 vaccine-strain (western topotype). Similarly BTV-10 isolates (IND2003/06; IND2005/04) show >99% identity in all genome segments, to the prototype BTV-10 (CA-8) strain from the USA. These data suggest repeated introductions of western BTV field and/or vaccine-strains into India, potentially linked to animal or vector-insect movements, or unauthorised use of 'live' South African or American BTV-vaccines in the country. The data presented will help improve nucleic acid based diagnostics for Indian serotypes/topotypes, as part of control strategies.

  4. Genomic epidemiology of Salmonella enterica serotype Enteritidis based on population structure of prevalent lineages

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  5. Complete genome sequence of hypervirulent and outbreak-associated Acinetobacter baumannii strain LAC-4: epidemiology, resistance genetic determinants and potential virulence factors

    PubMed Central

    Ou, Hong-Yu; Kuang, Shan N.; He, Xinyi; Molgora, Brenda M.; Ewing, Peter J.; Deng, Zixin; Osby, Melanie; Chen, Wangxue; Xu, H. Howard

    2015-01-01

    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

  6. Genomic Epidemiology of Clostridium botulinum Isolates from Temporally Related Cases of Infant Botulism in New South Wales, Australia.

    PubMed

    McCallum, Nadine; Gray, Timothy J; Wang, Qinning; Ng, Jimmy; Hicks, Leanne; Nguyen, Trang; Yuen, Marion; Hill-Cawthorne, Grant A; Sintchenko, Vitali

    2015-09-01

    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.

  7. Genomic Epidemiology of Clostridium botulinum Isolates from Temporally Related Cases of Infant Botulism in New South Wales, Australia

    PubMed Central

    Gray, Timothy J.; Wang, Qinning; Ng, Jimmy; Hicks, Leanne; Nguyen, Trang; Yuen, Marion; Hill-Cawthorne, Grant A.; Sintchenko, Vitali

    2015-01-01

    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. PMID:26109442

  8. Genomic Epidemiology of Clostridium botulinum Isolates from Temporally Related Cases of Infant Botulism in New South Wales, Australia.

    PubMed

    McCallum, Nadine; Gray, Timothy J; Wang, Qinning; Ng, Jimmy; Hicks, Leanne; Nguyen, Trang; Yuen, Marion; Hill-Cawthorne, Grant A; Sintchenko, Vitali

    2015-09-01

    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. PMID:26109442

  9. Genomic Epidemiology of Vibrio cholerae O1 Associated with Floods, Pakistan, 2010

    PubMed Central

    Shah, Muhammad Ali; Mutreja, Ankur; Thomson, Nicholas; Baker, Stephen; Parkhill, Julian; Dougan, Gordon; Bokhari, Habib

    2014-01-01

    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. PMID:24378019

  10. Complete Genome Sequence of Dyella thiooxydans ATSB10, a Thiosulfate-Oxidizing Bacterium Isolated from Sunflower Fields in South Korea

    PubMed Central

    Hwangbo, Kyeong; Um, Yurry; Chung, Hee; Yoo, Jemin; Kim, Ki Yoon; Madhaiyan, Munusamy; Sa, Tong Min

    2016-01-01

    Dyella thiooxydans ATSB10 (KACC 12756T = LMG 24673T) is a thiosulfate-oxidizing bacterium isolated from rhizosphere soils of sunflower plants. In this study, we completely sequenced the genome of D. thiooxydans ATSB10 and identified the genes involved in thiosulfate oxidation and the metabolism of aromatic intermediates. PMID:27340060

  11. Evaluation of an Optimal Epidemiological Typing Scheme for Legionella pneumophila with Whole-Genome Sequence Data Using Validation Guidelines.

    PubMed

    David, Sophia; Mentasti, Massimo; Tewolde, Rediat; Aslett, Martin; Harris, Simon R; Afshar, Baharak; Underwood, Anthony; Fry, Norman K; Parkhill, Julian; Harrison, Timothy G

    2016-08-01

    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

  12. Evaluation of an Optimal Epidemiological Typing Scheme for Legionella pneumophila with Whole-Genome Sequence Data Using Validation Guidelines

    PubMed Central

    Mentasti, Massimo; Tewolde, Rediat; Aslett, Martin; Harris, Simon R.; Afshar, Baharak; Underwood, Anthony; Harrison, Timothy G.

    2016-01-01

    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

  13. Full-genomic analysis of a human norovirus recombinant GII.12/13 novel strain isolated from South Korea.

    PubMed

    Won, Yu-Jung; Park, Jeong-Woong; Han, Sang-ha; Cho, Han-Gil; Kang, Lae-Hyung; Lee, Sung-Geun; Ryu, Sang-Ryeol; Paik, Soon-Young

    2013-01-01

    Norovirus (NoV) genogroups I and II are frequently recognized as the main causes of acute gastroenteritis and outbreaks of non-bacterial foodborne diseases. Furthermore, variants and recombinant strains of this virus are continuously emerging worldwide. The aim of this study was to identify NoV strains and to investigate and characterize rare genotypes. Stool samples (n = 500) were collected from patients with symptoms of acute gastroenteritis in Korea between December 2004 and November 2007. For analysis of the samples, rapid genotype screening was performed using reverse transcriptase-polymerase chain reaction. Full sequencing, using a newly designed set of 12 primers, revealed GII-12/13 strain. The partial sequence of GII-12/13 strain was compared with published NoV (GII-1 - 14) sequences targeting RdRp and capsid regions using phylogenetic analysis with the SimPlot program, which could evaluate recombination breakpoints. SimPlot analysis was also performed with the strain GII-12/Gifu-96/JPN (AB045603) for the RdRp region and with GII-13/G5175B-83/AUS(DQ379714) for the capsid region. NoV was detected in 19 of the 500 stool samples (3.8%). Genogroup GII-4 was found most frequently (n = 9, 1.8%), followed by GII-3 (n = 4, 0.8%), GII-6 (n = 3, 0.6%), GI-6 (n = 2, 0.4%), and GII-12/13 (n = 1, 0.2%). Importantly, we identified a novel NoV recombinant strain, C9-439 (KF289337), indicating potential risks, which suggested that, recombination occurred in the region between open reading frames 1 and 2 of the GII-12/13 strain and that breakpoints occurred in the polymerase region.

  14. Effects of smoking on the genetic risk of obesity: the population architecture using genomics and epidemiology study

    PubMed Central

    2013-01-01

    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

  15. Genomic Microbial Epidemiology Is Needed to Comprehend the Global Problem of Antibiotic Resistance and to Improve Pathogen Diagnosis.

    PubMed

    Wyrsch, Ethan R; Roy Chowdhury, Piklu; Chapman, Toni A; Charles, Ian G; Hammond, Jeffrey M; Djordjevic, Steven P

    2016-01-01

    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

  16. Genomic Microbial Epidemiology Is Needed to Comprehend the Global Problem of Antibiotic Resistance and to Improve Pathogen Diagnosis

    PubMed Central

    Wyrsch, Ethan R.; Roy Chowdhury, Piklu; Chapman, Toni A.; Charles, Ian G.; Hammond, Jeffrey M.; Djordjevic, Steven P.

    2016-01-01

    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

  17. Combined genome-wide linkage and association analyses of fasting glucose level in healthy twins and families of Korea.

    PubMed

    Suh, Young Ju; Kim, Sunghwan; Kim, So Hun; Park, Jia; Lim, Hyun Ae; Park, Hyun Ju; Choi, Hangseok; Ng, Daniel; Lee, Mi Kyeong; Nam, Moonsuk

    2013-03-01

    This study was undertaken to identify genetic polymorphisms that are associated with the risk of an elevated fasting glucose (FG) level using genome-wide analyses. We explored a quantitative trait locus (QTL) for FG level in a genome-wide study from a Korean twin-family cohort (the Healthy Twin Study) using a combined linkage and family-based association analysis approach. We investigated 1,754 individuals, which included 432 families and 219 pairs of monozygotic twins. Regions of chromosomes 2q23.3-2q31.1, 15q26.1-15q26.3, 16p12.1, and 20p13-20p12.2, were found to show evidence of linkage with FG level, and several markers in these regions were found to be significantly associated with FG level using family-based or general association tests. In particular, a single-nucleotide polymorphism (rs6138953) on the PTPRA gene in the 20p13 region (combined P = 1.8 × 10(-6)) was found to be associated with FG level, and the PRKCB1 gene (in 16p12.1) to be possibly associated with FG level. In conclusion, multiple regions of chromosomes 2q23.3-2q31.1, 15q26.1-15q26.3, 16p12.1, and 20p13-20p12.2 are associated with FG level in our Korean twin-family cohort. The combined approach of genome-wide linkage and family-based association analysis is useful to identify novel or known genetic regions concerning FG level in a family cohort study.

  18. HuGE Watch: tracking trends and patterns of published studies of genetic association and human genome epidemiology in near-real time.

    PubMed

    Yu, Wei; Wulf, Anja; Yesupriya, Ajay; Clyne, Melinda; Khoury, Muin Joseph; Gwinn, Marta

    2008-09-01

    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

  19. First Complete Genome Sequence of the Dutch Veterinary Coxiella burnetii Strain NL3262, Originating from the Largest Global Q Fever Outbreak, and Draft Genome Sequence of Its Epidemiologically Linked Chronic Human Isolate NLhu3345937

    PubMed Central

    Kuley, Runa; Smith, Hilde E.; Janse, Ingmar; Harders, Frank L.; Baas, Frank; Schijlen, Elio; Nabuurs-Franssen, Marrigje H.; Smits, Mari A.; Roest, Hendrik I. J.

    2016-01-01

    The largest global Q fever outbreak occurred in The Netherlands during 2007 to 2010. Goats and sheep were identified as the major sources of disease. Here, we report the first complete genome sequence of Coxiella burnetii goat outbreak strain NL3262 and that of an epidemiologically linked chronic human strain, both having the outbreak-related CbNL01 multilocus variable-number tandem-repeat analysis (MLVA) genotype. PMID:27103714

  20. First Complete Genome Sequence of the Dutch Veterinary Coxiella burnetii Strain NL3262, Originating from the Largest Global Q Fever Outbreak, and Draft Genome Sequence of Its Epidemiologically Linked Chronic Human Isolate NLhu3345937.

    PubMed

    Kuley, Runa; Smith, Hilde E; Janse, Ingmar; Harders, Frank L; Baas, Frank; Schijlen, Elio; Nabuurs-Franssen, Marrigje H; Smits, Mari A; Roest, Hendrik I J; Bossers, Alex

    2016-01-01

    The largest global Q fever outbreak occurred in The Netherlands during 2007 to 2010. Goats and sheep were identified as the major sources of disease. Here, we report the first complete genome sequence of ITALIC! Coxiella burnetiigoat outbreak strain NL3262 and that of an epidemiologically linked chronic human strain, both having the outbreak-related ITALIC! CbNL01multilocus variable-number tandem-repeat analysis (MLVA) genotype. PMID:27103714

  1. Traceback investigation for Salmonella contamination at egg processing plants in South Korea: prevalence, antibiotic resistance, and epidemiological tracing by rep-PCR fingerprinting.

    PubMed

    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

    2015-04-01

    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.

  2. Differences in pregnancy outcomes, prenatal care utilization, and maternal complications between teenagers and adult women in Korea: A nationwide epidemiological study.

    PubMed

    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

    2016-08-01

    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). PMID:27559960

  3. Henoch-Schonlein Purpura in Children Hospitalized at a Tertiary Hospital during 2004-2015 in Korea: Epidemiology and Clinical Management

    PubMed Central

    Lee, Yong Hee; Kim, Yu Bin; Koo, Ja Wook

    2016-01-01

    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

  4. Enabling high-throughput genotype-phenotype associations in the Epidemiologic Architecture for Genes Linked to Environment (EAGLE) project as part of the Population Architecture using Genomics and Epidemiology (PAGE) study.

    PubMed

    Bush, William S; Boston, Jonathan; Pendergrass, Sarah A; Dumitrescu, Logan; Goodloe, Robert; Brown-Gentry, Kristin; Wilson, Sarah; McClellan, Bob; Torstenson, Eric; Basford, Melissa A; Spencer, Kylee L; Ritchie, Marylyn D; Crawford, Dana C

    2013-01-01

    Genetic association studies have rapidly become a major tool for identifying the genetic basis of common human diseases. The advent of cost-effective genotyping coupled with large collections of samples linked to clinical outcomes and quantitative traits now make it possible to systematically characterize genotype-phenotype relationships in diverse populations and extensive datasets. To capitalize on these advancements, the Epidemiologic Architecture for Genes Linked to Environment (EAGLE) project, as part of the collaborative Population Architecture using Genomics and Epidemiology (PAGE) study, accesses two collections: the National Health and Nutrition Examination Surveys (NHANES) and BioVU, Vanderbilt University's biorepository linked to de-identified electronic medical records. We describe herein the workflows for accessing and using the epidemiologic (NHANES) and clinical (BioVU) collections, where each workflow has been customized to reflect the content and data access limitations of each respective source. We also describe the process by which these data are generated, standardized, and shared for meta-analysis among the PAGE study sites. As a specific example of the use of BioVU, we describe the data mining efforts to define cases and controls for genetic association studies of common cancers in PAGE. Collectively, the efforts described here are a generalized outline for many of the successful approaches that can be used in the era of high-throughput genotype-phenotype associations for moving biomedical discovery forward to new frontiers of data generation and analysis.

  5. Antiviral treatment of influenza in South Korea.

    PubMed

    Choe, Young June; Lee, Hyunju; Lee, Hoan Jong; Choi, Eun Hwa

    2015-06-01

    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.

  6. Whole-Genome Sequencing and Epidemiological Analysis Do Not Provide Evidence for Cross-transmission of Mycobacterium abscessus in a Cohort of Pediatric Cystic Fibrosis Patients

    PubMed Central

    Harris, Kathryn A.; Underwood, Anthony; Kenna, Dervla T. D.; Brooks, Anthony; Kavaliunaite, Ema; Kapatai, Georgia; Tewolde, Rediat; Aurora, Paul; Dixon, Garth

    2015-01-01

    Background. Mycobacterium abscessus has emerged as a major pathogen in cystic fibrosis (CF) patients and has been associated with poor clinical outcomes, particularly following lung transplant. We investigated the acquisition of this bacterium in a cohort of pediatric CF patients. Methods. Demographic and patient location data were used to uncover epidemiological links between patients with genetically related strains of M. abscessus that had been previously typed by variable-number tandem repeat profiling. Whole-genome sequencing was applied to 27 M. abscessus isolates from the 20 patients in this cohort to provide definitive data on the genetic relatedness of strains. Results. Whole-genome sequencing data demonstrated that M. abscessus isolates from 16 patients were unrelated, differing by at least 34 single-nucleotide polymorphisms (SNPs) from any other isolate, suggesting that independent acquisition events have occurred. Only 2 clusters of very closely related (<25 SNPs) isolates from different patients were seen. The first cluster contained 8 isolates, differing by a maximum of 17 SNPs, from a sibling pair who had intense exposure to each other both inside and outside the hospital. The second cluster contained 3 isolates, differing by a maximum of 24 SNPs, from 2 individuals with no apparent epidemiological links. Conclusions. We have not demonstrated cross-transmission of M. abscessus within our hospital, except between 1 sibling pair. Alternative routes of acquisition of M. abscessus infection, in particular the environment, require further investigation. PMID:25452595

  7. Integrating understanding of epidemiology and genomics in B-cell non-Hodgkin lymphoma as a pathway to novel management strategies.

    PubMed

    Glass, Samantha; Phan, Anh; Williams, Jessica N; Flowers, Christopher R; Koff, Jean L

    2016-03-01

    Non-Hodgkin lymphomas include a biologically and clinically heterogeneous group of cancers distinguished by genetics, histology, and treatment outcomes. New discoveries regarding the genomic alterations and epidemiological exposures associated with these lymphomas have enhanced our understanding of factors that contribute to lymphomagenesis for specific subtypes. We explore the impact of normal B-cell biology engineered for recognizing a wide variety of antigens on the development of specific lymphoma subtypes, review lymphoma genetics, and examine the epidemiology of B-cell NHLs including recent investigations of risk factors for particular lymphoma subtypes based on large pooled analyses. Burkitt lymphoma, an aggressive form of B-cell NHL involving translocation of the MYC gene and an immunoglobulin gene has been associated with a history of eczema, hepatitis C, and occupation as a cleaner. Increased risk of diffuse large B-cell lymphoma has been associated with increased young adult body mass index, history of B-cell-activating autoimmune diseases, hepatitis C, and several single nucleotide variants involving the human leukocyte antigen (HLA) region of chromosome 6 and non-HLA loci near EXOC2, PVT1, MYC, and NCOA1. Tumor sequencing studies suggest that multiple pathways are involved in the development of DLBCL. Additional studies of epidemiological exposures, genome wide associations, and tumor sequencing in follicular, lymphoplasmacytic, marginal zone, and mantle cell lymphoma demonstrate overlapping areas of increased risk factors and unique factors for specific subtypes. Integrating these findings is important for constructing comprehensive models of NHL pathogenesis, which could yield novel targets for therapy and strategies for lymphoma prevention in certain populations. PMID:27115168

  8. Special Education in Korea.

    ERIC Educational Resources Information Center

    Kim, Byung Ha, Ed.; Yeo, Kwang Eung

    The text on special education in Korea is divided into four major sections--a brief history of special education in Korea, the present status of special education in Korea, the special education plan of the Young Kwang Educational Foundation, and directory of schools and classes for the exceptional in Korea. Topics covered include the following:…

  9. Cancer Epidemiology Matters Blog - 2013 Archive

    Cancer.gov

    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.

  10. Cancer Epidemiology Matters Blog - 2012 Archive

    Cancer.gov

    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.

  11. Cancer Epidemiology Matters Blog - 2015 Archive

    Cancer.gov

    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.

  12. Cancer Epidemiology Matters Blog - 2014 Archive

    Cancer.gov

    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.

  13. Descriptive Epidemiology and Whole Genome Sequencing Analysis for an Outbreak of Bovine Tuberculosis in Beef Cattle and White-Tailed Deer in Northwestern Minnesota

    PubMed Central

    Glaser, Linda; Carstensen, Michelle; Shaw, Sheryl; Robbe-Austerman, Suelee; Wunschmann, Arno; Grear, Dan; Stuber, Tod; Thomsen, Bruce

    2016-01-01

    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

  14. Descriptive Epidemiology and Whole Genome Sequencing Analysis for an Outbreak of Bovine Tuberculosis in Beef Cattle and White-Tailed Deer in Northwestern Minnesota.

    PubMed

    Glaser, Linda; Carstensen, Michelle; Shaw, Sheryl; Robbe-Austerman, Suelee; Wunschmann, Arno; Grear, Dan; Stuber, Tod; Thomsen, Bruce

    2016-01-01

    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.

  15. Descriptive Epidemiology and Whole Genome Sequencing Analysis for an Outbreak of Bovine Tuberculosis in Beef Cattle and White-Tailed Deer in Northwestern Minnesota.

    PubMed

    Glaser, Linda; Carstensen, Michelle; Shaw, Sheryl; Robbe-Austerman, Suelee; Wunschmann, Arno; Grear, Dan; Stuber, Tod; Thomsen, Bruce

    2016-01-01

    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

  16. Subtype-independent near full-length HIV-1 genome sequencing and assembly to be used in large molecular epidemiological studies and clinical management

    PubMed Central

    Grossmann, Sebastian; Nowak, Piotr; Neogi, Ujjwal

    2015-01-01

    Introduction HIV-1 near full-length genome (HIV-NFLG) sequencing from plasma is an attractive multidimensional tool to apply in large-scale population-based molecular epidemiological studies. It also enables genotypic resistance testing (GRT) for all drug target sites allowing effective intervention strategies for control and prevention in high-risk population groups. Thus, the main objective of this study was to develop a simplified subtype-independent, cost- and labour-efficient HIV-NFLG protocol that can be used in clinical management as well as in molecular epidemiological studies. Methods Plasma samples (n=30) were obtained from HIV-1B (n=10), HIV-1C (n=10), CRF01_AE (n=5) and CRF01_AG (n=5) infected individuals with minimum viral load >1120 copies/ml. The amplification was performed with two large amplicons of 5.5 kb and 3.7 kb, sequenced with 17 primers to obtain HIV-NFLG. GRT was validated against ViroSeq™ HIV-1 Genotyping System. Results After excluding four plasma samples with low-quality RNA, a total of 26 samples were attempted. Among them, NFLG was obtained from 24 (92%) samples with the lowest viral load being 3000 copies/ml. High (>99%) concordance was observed between HIV-NFLG and ViroSeq™ when determining the drug resistance mutations (DRMs). The N384I connection mutation was additionally detected by NFLG in two samples. Conclusions Our high efficiency subtype-independent HIV-NFLG is a simple and promising approach to be used in large-scale molecular epidemiological studies. It will facilitate the understanding of the HIV-1 pandemic population dynamics and outline effective intervention strategies. Furthermore, it can potentially be applicable in clinical management of drug resistance by evaluating DRMs against all available antiretrovirals in a single assay. PMID:26115688

  17. Epidemiological fingerprinting of Enterobacter cloacae by small-fragment restriction endonuclease analysis and pulsed-field gel electrophoresis of genomic restriction fragments.

    PubMed Central

    Haertl, R; Bandlow, G

    1993-01-01

    A cluster of infections caused by Enterobacter cloacae was observed among preterm neonates in a neonatal intensive care unit (NICU) of a pediatric hospital in Osnabrück, Germany. The presence of similar antimicrobial susceptibility patterns among the bacterial isolates prompted an investigation to determine whether a limited spread of a single strain existed. All 12 E. cloacae isolates from the NICU and 50 nonrelated strains were fingerprinted by small-fragment restriction endonuclease analysis (SF-REA) of EcoRI DNA digests. Selected isolates were further characterized by pulsed-field gel electrophoresis (PFGE) of NotI- or XbaI-generated genomic restriction fragments. Epidemiologically unrelated strains were clearly discriminated by both methods. Results achieved by SF-REA and PFGE revealed that of the 12 isolates from the NICU, 11 belonged to the same genotypic cluster. Since all reagents and equipment for both techniques are commercially available, DNA fingerprinting by SF-REA or PFGE is proposed as a useful tool in the microbiology laboratory for investigating the epidemiological relatedness of E. cloacae strains of clinical and environmental origin. Images PMID:8093251

  18. Cutaneous Lymphoma in Korea: A Nationwide Retrospective Study.

    PubMed

    Lee, Hyun Soo; Suh, Kee Suck; Lee, Dong-Youn; Cho, Kwang Hyun; Oh, Sang Ho; Kim, Soo-Chan; Lee, Seok-Jong; Shin, Dong Hoon; Yoon, Tae Young; Won, Young Ho; Kim, You Chan

    2016-05-01

    The epidemiological and clinicopathological features of cutaneous lymphoma may vary by geographical area. However, only a few large-scale epidemiological studies of cutaneous lymphoma have been performed, mainly in the USA and Europe. This aim of this study was to determine the recent characteristics of cutaneous lymphoma in Korea according to the WHO/EORTC classification. A total of 422 patients with newly diagnosed cutaneous lymphoma from January 2009 to December 2013 comprising 293 cases of mature T-cell and natural killer (NK)-cell lymphoma and 39 cases of mature B-cell lymphoma were retrospectively reviewed. The incidence of mature B-cell lymphoma was lower in Korea than in Europe and the USA. Diffuse large B-cell lymphoma was more prevalent in Korea than in Western countries. The incidence of extranodal NK/T-cell lymphoma, nasal-type was higher in Korea than in Western countries and Japan. PMID:26560051

  19. Complete Genome Sequence of the Proteorhodopsin-Containing Marine Flavobacterium Dokdonia donghaensis DSW-1T, Isolated from Seawater off Dokdo in the East Sea (Sea of Korea).

    PubMed

    Kim, Kitae; Kwon, Soon-Kyeong; Yoon, Jung-Hoon; Kim, Jihyun F

    2016-01-01

    Dokdonia spp. have been used for investigating the lifestyles of proteorhodopsin-containing photoheterotrophs and for understanding marine photobiology. Here, we report the complete genome sequence of Dokdonia donghaensis DSW-1(T) using the PacBio sequencing platform. It should provide a valuable resource for comparative genomic studies of marine life harboring microbial rhodopsins among others. PMID:27491981

  20. Complete Genome Sequence of the Proteorhodopsin-Containing Marine Flavobacterium Dokdonia donghaensis DSW-1T, Isolated from Seawater off Dokdo in the East Sea (Sea of Korea)

    PubMed Central

    Kim, Kitae; Kwon, Soon-Kyeong; Yoon, Jung-Hoon

    2016-01-01

    Dokdonia spp. have been used for investigating the lifestyles of proteorhodopsin-containing photoheterotrophs and for understanding marine photobiology. Here, we report the complete genome sequence of Dokdonia donghaensis DSW-1T using the PacBio sequencing platform. It should provide a valuable resource for comparative genomic studies of marine life harboring microbial rhodopsins among others. PMID:27491981

  1. Whole Genome Sequence Analysis Using JSpecies Tool Establishes Clonal Relationships between Listeria monocytogenes Strains from Epidemiologically Unrelated Listeriosis Outbreaks.

    PubMed

    Burall, Laurel S; Grim, Christopher J; Mammel, Mark K; Datta, Atin R

    2016-01-01

    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 two

  2. Whole Genome Sequence Analysis Using JSpecies Tool Establishes Clonal Relationships between Listeria monocytogenes Strains from Epidemiologically Unrelated Listeriosis Outbreaks

    PubMed Central

    Burall, Laurel S.; Grim, Christopher J.; Mammel, Mark K.; Datta, Atin R.

    2016-01-01

    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

  3. Targeted sequencing in candidate genes for atrial fibrillation: The Cohorts for Heart and Aging Research in Genomic Epidemiology Targeted Sequencing Study

    PubMed Central

    Lin, Honghuang; Sinner, Moritz F.; Brody, Jennifer A.; Arking, Dan E.; Lunetta, Kathryn L.; Rienstra, Michiel; Lubitz, Steven A.; Magnani, Jared W.; Sotoodehnia, Nona; McKnight, Barbara; McManus, David D.; Boerwinkle, Eric; Psaty, Bruce M.; Rotter, Jerome I.; Bis, Joshua C.; Gibbs, Richard A.; Muzny, Donna; Kovar, Christie L.; Morrison, Alanna C.; Gupta, Mayetri; Folsom, Aaron R.; Kääb, Stefan; Heckbert, Susan R.; Alonso, Alvaro; Ellinor, Patrick T.; Benjamin, Emelia J.

    2014-01-01

    Background Genome-wide association studies (GWAS) have identified common genetic variants that predispose to atrial fibrillation (AF). It is unclear whether rare and low-frequency variants in genes implicated by such GWAS confer additional risk of AF. Objective To study the association of genetic variants with AF at GWAS top loci. Methods In the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Targeted Sequencing Study, we selected and sequenced 77 target gene regions from GWAS loci of complex diseases or traits, including 4 genes hypothesized to be related to AF (PRRX1, CAV1, CAV2, and ZFHX3). Sequencing was performed in participants with (n = 948) and without (n = 3330) AF from the Atherosclerosis Risk in Communities Study, the Cardiovascular Health Study, the Framingham Heart Study, and the Massachusetts General Hospital. Results One common variant (rs11265611; P = 1.70 × 10−6) intronic to IL6R (interleukin-6 receptor gene) was significantly associated with AF after Bonferroni correction (odds ratio 0.70; 95% confidence interval 0.58–0.85). The variant was not genotyped or imputed by prior GWAS, but it is in linkage disequilibrium (r2 = .69) with the single-nucleotide polymorphism, with the strongest association with AF so far at this locus (rs4845625). In the rare variant joint analysis, damaging variants within the PRRX1 region showed significant association with AF after Bonferroni correction (P = .01). Conclusions We identified 1 common single-nucleotide polymorphism and 1 gene region that were significantly associated with AF. Future sequencing efforts with larger sample sizes and more comprehensive genome coverage are anticipated to identify additional AF-related variants. PMID:24239840

  4. Pleiotropic and Sex-Specific Effects of Cancer GWAS SNPs on Melanoma Risk in the Population Architecture Using Genomics and Epidemiology (PAGE) Study

    PubMed Central

    Kocarnik, Jonathan M.; Park, S. Lani; Han, Jiali; Dumitrescu, Logan; Cheng, Iona; Wilkens, Lynne R.; Schumacher, Fredrick R.; Kolonel, Laurence; Carlson, Chris S.; Crawford, Dana C.; Goodloe, Robert J.; Dilks, Holli H.; Baker, Paxton; Richardson, Danielle; Matise, Tara C.; Ambite, José Luis; Song, Fengju; Qureshi, Abrar A.; Zhang, Mingfeng; Duggan, David; Hutter, Carolyn; Hindorff, Lucia; Bush, William S.; Kooperberg, Charles; Le Marchand, Loic; Peters, Ulrike

    2015-01-01

    Background Several regions of the genome show pleiotropic associations with multiple cancers. We sought to evaluate whether 181 single-nucleotide polymorphisms previously associated with various cancers in genome-wide association studies were also associated with melanoma risk. Methods We evaluated 2,131 melanoma cases and 20,353 controls from three studies in the Population Architecture using Genomics and Epidemiology (PAGE) study (EAGLE-BioVU, MEC, WHI) and two collaborating studies (HPFS, NHS). Overall and sex-stratified analyses were performed across studies. Results We observed statistically significant associations with melanoma for two lung cancer SNPs in the TERT-CLPTM1L locus (Bonferroni-corrected p<2.8x10-4), replicating known pleiotropic effects at this locus. In sex-stratified analyses, we also observed a potential male-specific association between prostate cancer risk variant rs12418451 and melanoma risk (OR=1.22, p=8.0x10-4). No other variants in our study were associated with melanoma after multiple comparisons adjustment (p>2.8e-4). Conclusions We provide confirmatory evidence of pleiotropic associations with melanoma for two SNPs previously associated with lung cancer, and provide suggestive evidence for a male-specific association with melanoma for prostate cancer variant rs12418451. This SNP is located near TPCN2, an ion transport gene containing SNPs which have been previously associated with hair pigmentation but not melanoma risk. Previous evidence provides biological plausibility for this association, and suggests a complex interplay between ion transport, pigmentation, and melanoma risk that may vary by sex. If confirmed, these pleiotropic relationships may help elucidate shared molecular pathways between cancers and related phenotypes. PMID:25789475

  5. Draft genome of Leisingera aquaemixtae CECT 8399T, a member of the Roseobacter clade isolated from a junction of fresh and ocean water in Jeju Island, South Korea

    PubMed Central

    Rodrigo-Torres, Lidia; Pujalte, María J.; Arahal, David R.

    2016-01-01

    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

  6. A genome-wide association study for venous thromboembolism: the extended Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium

    PubMed Central

    Pankratz, Nathan; Leebeek, Frank W.; Paré, Guillaume; de Andrade, Mariza; Tzourio, Christophe; Psaty, Bruce M.; Basu, Saonli; Ruiter, Rikje; Rose, Lynda; Armasu, Sebastian M.; Lumley, Thomas; Heckbert, Susan R.; Uitterlinden, André G.; Lathrop, Mark; Rice, Kenneth M.; Cushman, Mary; Hofman, Albert; Lambert, Jean-Charles; Glazer, Nicole L.; Pankow, James S.; Witteman, Jacqueline C.; Amouyel, Philippe; Bis, Joshua C.; Bovill, Edwin G.; Kong, Xiaoxiao; Tracy, Russell P.; Boerwinkle, Eric; Rotter, Jerome I.; Trégouët, David-Alexandre; Loth, Daan W.

    2014-01-01

    Venous thromboembolism (VTE) is a common, heritable disease resulting in high rates of hospitalization and mortality. Yet few associations between VTE and genetic variants, all in the coagulation pathway, have been established. To identify additional genetic determinants of VTE, we conducted a 2-stage genome-wide association study (GWAS) among individuals of European ancestry in the extended CHARGE VTE consortium. The discovery GWAS comprised 1,618 incident VTE cases out of 44,499 participants from six community-based studies. Genotypes for genome-wide single-nucleotide polymorphisms (SNPs) were imputed to ~2.5 million SNPs in HapMap and association with VTE assessed using study-design appropriate regression methods. Meta-analysis of these results identified two known loci, in F5 and ABO. Top 1,047 tag SNPs (p≤0.0016) from the discovery GWAS were tested for association in an additional 3,231 cases and 3,536 controls from three case-control studies. In the combined data from these two stages, additional genome-wide significant associations were observed on 4q35 at F11 (top SNP rs4253399, intronic to F11) and on 4q28 at FGG (rs6536024, 9.7 kb from FGG) (p<5.0×10−13 for both). The associations at the FGG locus were not completely explained by previously reported variants. Loci at or near SUSD1 and OTUD7A showed borderline yet novel associations (p<5.0×10-6) and constitute new candidate genes. In conclusion, this large GWAS replicated key genetic associations in F5 and ABO, and confirmed the importance of F11 and FGG loci for VTE. Future studies are warranted to better characterize the associations with F11 and FGG and to replicate the new candidate associations. PMID:23650146

  7. The future of epidemiology.

    PubMed

    Ness, Roberta B; Andrews, Elizabeth B; Gaudino, James A; Newman, Anne B; Soskolne, Colin L; Stürmer, Til; Wartenberg, Daniel E; Weiss, Stanley H

    2009-11-01

    In this article, the authors discuss current challenges and opportunities in epidemiology that will affect the field's future. Epidemiology is commonly considered the methodologic backbone for the fields of public health and outcomes research because its practitioners describe patterns of disease occurrence, identify risk factors and etiologic determinants, and demonstrate the usefulness of interventions. Like most aspects of science, epidemiology is in rapid flux. Several factors that are influencing and will continue to influence epidemiology and the health of the public include factors fundamental to framing the discipline of epidemiology (i.e., its means of communication, its methodologies, its access to data, its values, its population perspective), factors relating to scientific advances (e.g., genomics, comparative effectiveness in therapeutics), and factors shaping human health (e.g., increasing globalism, the environment, disease and lifestyle, demographics, infectious disease). PMID:19858828

  8. [Opportunity and challenge on molecular epidemiology].

    PubMed

    Duan, G C; Chen, S Y

    2016-08-10

    Molecular epidemiology, a branch of epidemiology, combines the theories and methods, both in epidemiology and molecular biology. Molecular epidemiology mainly focuses on biological markers, describing the distribution, occurrence, development and prognosis of diseases at the molecular level. The completion of Human Genome Project and rapid development of Precision Medicine and Big Data not only offer the new development opportunities but also bring about a higher demand and new challenge for molecular epidemiology. PMID:27539332

  9. Complete genome and molecular epidemiological data infer the maintenance of rabies among kudu (Tragelaphus strepsiceros) in Namibia.

    PubMed

    Scott, Terence P; Fischer, Melina; Khaiseb, Siegfried; Freuling, Conrad; Höper, Dirk; Hoffmann, Bernd; Markotter, Wanda; Müller, Thomas; Nel, Louis H

    2013-01-01

    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

  10. Complete genome and molecular epidemiological data infer the maintenance of rabies among kudu (Tragelaphus strepsiceros) in Namibia.

    PubMed

    Scott, Terence P; Fischer, Melina; Khaiseb, Siegfried; Freuling, Conrad; Höper, Dirk; Hoffmann, Bernd; Markotter, Wanda; Müller, Thomas; Nel, Louis H

    2013-01-01

    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.

  11. 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

    PubMed Central

    Song, Sun Ok; Nam, Joo Young; Park, Kyeong Hye; Yoon, Ji-Hae; Son, Kyung-Mi; Ko, Young; Lim, Dong-Ha

    2016-01-01

    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

  12. Genome-wide single nucleotide polymorphism-based assay for high-resolution epidemiological analysis of the methicillin-resistant Staphylococcus aureus hospital clone EMRSA-15.

    PubMed

    Holmes, A; McAllister, G; McAdam, P R; Hsien Choi, S; Girvan, K; Robb, A; Edwards, G; Templeton, K; Fitzgerald, J R

    2014-02-01

    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.

  13. Sample Cancer Epidemiology Grant Applications

    Cancer.gov

    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.

  14. 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.

    PubMed

    Pettengill, Emily A; Pettengill, James B; Binet, Rachel

    2015-01-01

    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. PMID:26834722

  15. 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

    PubMed Central

    Pettengill, Emily A.; Pettengill, James B.; Binet, Rachel

    2016-01-01

    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. PMID:26834722

  16. 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.

    PubMed

    Pettengill, Emily A; Pettengill, James B; Binet, Rachel

    2015-01-01

    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.

  17. Middle East Respiratory Syndrome Coronavirus Outbreak in the Republic of Korea, 2015

    PubMed Central

    2015-01-01

    Objectives The outbreak of Middle East respiratory syndrome coronavirus (MERS-CoV) infection in the Republic of Korea started from the index case who developed fever after returning from the Middle East. He infected 26 cases in Hospital C, and consecutive nosocomial transmission proceeded throughout the nation. We provide an epidemiologic description of the outbreak, as of July 2015. Methods Epidemiological research was performed by direct interview of the confirmed patients and reviewing medical records. We also analyzed the incubation period, serial interval, the characteristics of superspreaders, and factors associated with mortality. Full genome sequence was obtained from sputum specimens of the index patient. Results A total of 186 confirmed patients with MERS-CoV infection across 16 hospitals were identified in the Republic of Korea. Some 44.1% of the cases were patients exposed in hospitals, 32.8% were caregivers, and 13.4% were healthcare personnel. The most common presenting symptom was fever and chills. The estimated incubation period was 6.83 days and the serial interval was 12.5 days. A total of 83.2% of the transmission events were epidemiologically linked to five superspreaders, all of whom had pneumonia at presentation and contacted hundreds of people. Older age [odds ratio (OR) = 4.86, 95% confidence interval (CI) 1.90–12.45] and underlying respiratory disease (OR = 4.90, 95% CI 1.64–14.65) were significantly associated with mortality. Phylogenetic analysis showed that the MERS-CoV of the index case clustered closest with a recent virus from Riyadh, Saudi Arabia. Conclusion A single imported MERS-CoV infection case imposed a huge threat to public health and safety. This highlights the importance of robust preparedness and optimal infection prevention control. The lessons learned from the current outbreak will contribute to more up-to-date guidelines and global health security. PMID:26473095

  18. [Electrophoretic karyotypes and genomic DNA restriction fragment analysis: their usefulness as tools in the epidemiological study of Candid parapsilosis].

    PubMed

    Perrotta, D; Rodero, L; Demkura, H; Canteros, C; Davel, G

    2002-01-01

    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.

  19. Tackling Drug Resistant Infection Outbreaks of Global Pandemic Escherichia coli ST131 Using Evolutionary and Epidemiological Genomics

    PubMed Central

    Downing, Tim

    2015-01-01

    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.

  20. Tackling Drug Resistant Infection Outbreaks of Global Pandemic Escherichia coli ST131 Using Evolutionary and Epidemiological Genomics

    PubMed Central

    Downing, Tim

    2015-01-01

    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

  1. Occupational Skin Diseases in Korea

    PubMed Central

    Kim, Min-Gi

    2010-01-01

    Skin disease is the most common occupational disease, but the reported number is small in Korea due to a difficulty of detection and diagnosis in time. We described various official statistics and data from occupational skin disease surveillance system, epidemiological surveys and cases published in scientific journals. Until 1981, 2,222 cases of occupational skin disease were reported by Korean employee's regular medical check-up, accounting for 4.9% of the total occupational diseases. There was no subsequent official statistics to figure out occupational skin diseases till 1998. From 1999, the Korea Occupational Safety and Health Agency (KOSHA) published the number of occupational skin diseases through the statistics of Cause Investigation for Industrial Accidents. A total of 301 cases were reported from 1999 to 2007. Recent one study showed the figures of compensated occupational skin diseases. Many of them belonged to daily-paid workers in the public service, especially forestry workers. Also, it described the interesting cases such as vitiligo and trichloroethylene-induced Stevens-Johnson Syndrome. Skin diseases are still important though the number of cases has decreased, and therefore it is recommended to grasp the status of occupational skin diseases through continuous surveillance system and to make policy protecting high-risk group. PMID:21258591

  2. Genomic analysis and pathogenic characteristics of Type 2 porcine reproductive and respiratory syndrome virus nsp2 deletion strains isolated in Korea.

    PubMed

    Choi, Hwan-Won; Nam, Eeuri; Lee, Yoo Jin; Noh, Yun-Hee; Lee, Seung-Chul; Yoon, In-Joong; Kim, Hyun-Soo; Kang, Shien-Young; Choi, Young-Ki; Lee, Changhee

    2014-06-01

    Porcine reproductive and respiratory syndrome virus (PRRSV) is a globally ubiquitous swine virus that exhibits genetic and pathogenic heterogeneity among isolates. The present study was conducted to determine the complete genome sequence and pathogenicity of two Korean type 2 PRRSV nonstructural protein 2 (nsp2) deletion mutants, CA-2 and KNU-12-KJ4. The full-length genomes of CA-2 and KNU-12-KJ4 were determined to be 15,018 and 15,019 nucleotides in length, excluding the poly(A) tail, respectively, which were 393- or 392-nucleotide shorter than that of the type 2 NA prototype strain VR-2332 due to the presence of notable large deletions within the nsp2 gene. The genomes of CA-2 and KNU-12-KJ4 consisted of a 189- or 190-nucleotide 5' untranslated region (UTR), a 14,677-nucleotide protein-coding region, and a 151-nucleotide 3' UTR. Whole genome evaluation revealed that the nucleotide sequences of CA-2 and KNU-12-KJ4 are most similar to each other (10.7% sequence divergence), and then to the Korean strain CA-1 (11.3% sequence divergence) and the US strain MN184C (13.1% sequence divergence), respectively. To evaluate the in vitro immunity of nsp2 deletion variants, we sought to explore alteration of inflammatory cytokine and chemokine expression in PAM-pCD163 cells infected with each virus strain using quantitative real-time RT-PCR. Cytokine genes including IL-8, IL-10, and TNF-α, and chemokines such as MCP-1 and RANTES were found to be significantly elevated in nsp2 deletion virus-infected PAM cells. In contrast, expression of interferons (IFN-β, γ, and λ) and antiviral genes including ISG-15, -54, and -56 were unchanged or down-regulated in PAM cells infected with the nsp2 deletion mutants. Animal studies to assess the pathogenicity of nsp2 deletion PRRSVs demonstrated that both CA-2 and KNU-12-KJ4 strains notably produce weight loss in infected pigs. Furthermore, the nsp2 deletion mutants replicated well in pigs with significantly increased and prolonged

  3. The Clinical and Laboratory Characteristics of Patients with Chronic Hepatitis B Using Current or Past Antiviral Therapy in Korea: A Multi-Center, Nation-Wide, Cross-Sectional Epidemiologic Study

    PubMed Central

    Choi, Moon Seok; Sinn, Dong Hyun; Kim, Su-A; Lee, Yil Seob; Choi, Won

    2012-01-01

    Background/Aims The proper assessment of the current disease status of patients with chronic hepatitis B would be valuable for establishing optimal management strategies. Methods The clinical and laboratory characteristics of 2,954 patients with current or previous antiviral treatment (46.2±10.8 years, 69.7% male) enrolled from 46 referral hospitals and 129 local hospitals or clinics throughout Korea were analyzed. Results The disease status included chronic hepatitis, cirrhosis, and hepatocellular carcinoma in 79.9%, 16.4%, and 3.7% of the patients, respectively. The major mode of hepatitis B virus (HBV) infection was vertical transmission. The hepatitis C virus (HCV) co-infection rate was 1.5%; however, only 50.8% of patients were evaluated for HCV. The use of herbal or complementary medicines was reported in 33.5% of the patients. The majority of patients (97.6%) were treated with oral nucleoside/nucleotide analogues. Several characteristics were different between the patients treated at referral hospitals and local hospitals/clinics, including the disease state, choice of antiviral drug, and methods of HBV DNA measurement. Conclusions This study provides a comprehensive picture of the clinical and laboratory characteristics of patients treated in Korea. Efforts to optimize management strategies are warranted. PMID:22570755

  4. English Teaching Profile: Korea.

    ERIC Educational Resources Information Center

    British Council, London (England). English Language and Literature Div.

    The role and status of English instruction in Korea is outlined. The role of English in Korea as a whole, English instruction within the educational system, language teacher training, textbook use, educational administration, educational development and planning, English instruction outside of the educational system, British and American support…

  5. The Geography of Korea.

    ERIC Educational Resources Information Center

    Park, Young-Han

    1988-01-01

    Briefly surveys the geography of both North and South Korea, examining mountain ranges, rivers, soil, and climate. Also discusses the economic activities of South Korea, including industrialization, transportation, population, and the urban system. Provides a map of the Korean peninsula and a table of land area and population by province. (GEA)

  6. 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.

    PubMed

    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

    2014-01-01

    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

  7. Circular epidemiology.

    PubMed

    Kuller, L H

    1999-11-01

    Circular epidemiology can be defined as the continuation of specific types of epidemiologic studies beyond the point of reasonable doubt of the true existence of an important association or the absence of such an association. Circular epidemiology is an extreme example of studies of the consistency of associations. A basic problem for epidemiology is the lack of a systematic approach to acquiring new knowledge to reach a goal of improving public health and preventive medicine. For epidemiologists, research support unfortunately is biased toward the continued study of already proven hypotheses. Circular epidemiology, however, freezes at one point in the evolution of epidemiologic studies, failing to move from descriptive to analytical case-control and longitudinal studies, for example, to experimental, clinical trials. Good epidemiology journals are filled with very well-conducted epidemiologic studies that primarily repeat the obvious or are variations on the theme.

  8. Q&A: Muin Khoury on cancer epidemiology.

    PubMed

    Khoury, Muin J; Rose, Suzanne

    2014-02-01

    Muin J. Khoury, MD, PhD, director of the Centers for Disease Control and Prevention's Office of Public Health Genomics and head of the National Cancer Institute's Epidemiology and Genomics Research Program in the Division of Cancer Control and Population Sciences, talks about challenges and opportunities in cancer epidemiology research and efforts in the epidemiology community to transform the field.

  9. Genetic characterization and evolutionary analysis of Newcastle disease virus isolated from domestic duck in South Korea.

    PubMed

    Gaikwad, Satish; Kim, Ji-Ye; Lee, Hyun-Jeong; Jung, Suk Chan; Choi, Kang-Seuk

    2016-03-15

    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.

  10. Terrorism in South Korea.

    PubMed

    Wang, Soon Joo; Choi, Jin Tae; Arnold, Jeffrey

    2003-01-01

    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.

  11. Terrorism in South Korea.

    PubMed

    Wang, Soon Joo; Choi, Jin Tae; Arnold, Jeffrey

    2003-01-01

    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. PMID:15074497

  12. Genome-wide analysis of copy number variations reveals that aging processes influence body fat distribution in Korea Associated Resource (KARE) cohorts.

    PubMed

    Lee, Bo-Young; Shin, Dong Hyun; Cho, Seoae; Seo, Kang-Seok; Kim, Heebal

    2012-11-01

    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

  13. China and Korea

    Atmospheric Science Data Center

    2013-04-16

    ... article title:  Dust Obscures Liaoning Province, China     View Larger Image ... acquired 16 days apart, covers the Liaoning region of China and parts of northern and western Korea. They contrast a relatively clear ...

  14. Obstructive Sleep Apnea Is Associated with Elevated High Sensitivity C-Reactive Protein Levels Independent of Obesity: Korean Genome and Epidemiology Study

    PubMed Central

    Kim, Jinkwan; Lee, Seok Jun; Choi, Kyung-Mee; Lee, Seung Ku; Yoon, Dae Wui; Lee, Seung Gwan; Shin, Chol

    2016-01-01

    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

  15. Genome-wide association study of white blood cell count in 16,388 African Americans: the continental origins and genetic epidemiology network (COGENT).

    PubMed

    Reiner, Alexander P; Lettre, Guillaume; Nalls, Michael A; Ganesh, Santhi K; Mathias, Rasika; Austin, Melissa A; Dean, Eric; Arepalli, Sampath; Britton, Angela; Chen, Zhao; Couper, David; Curb, J David; Eaton, Charles B; Fornage, Myriam; Grant, Struan F A; Harris, Tamara B; Hernandez, Dena; Kamatini, Naoyuki; Keating, Brendan J; Kubo, Michiaki; LaCroix, Andrea; Lange, Leslie A; Liu, Simin; Lohman, Kurt; Meng, Yan; Mohler, Emile R; Musani, Solomon; Nakamura, Yusuke; O'Donnell, Christopher J; Okada, Yukinori; Palmer, Cameron D; Papanicolaou, George J; Patel, Kushang V; Singleton, Andrew B; Takahashi, Atsushi; Tang, Hua; Taylor, Herman A; Taylor, Kent; Thomson, Cynthia; Yanek, Lisa R; Yang, Lingyao; Ziv, Elad; Zonderman, Alan B; Folsom, Aaron R; Evans, Michele K; Liu, Yongmei; Becker, Diane M; Snively, Beverly M; Wilson, James G

    2011-06-01

    Total white blood cell (WBC) and neutrophil counts are lower among individuals of African descent due to the common African-derived "null" variant of the Duffy Antigen Receptor for Chemokines (DARC) gene. Additional common genetic polymorphisms were recently associated with total WBC and WBC sub-type levels in European and Japanese populations. No additional loci that account for WBC variability have been identified in African Americans. In order to address this, we performed a large genome-wide association study (GWAS) of total WBC and cell subtype counts in 16,388 African-American participants from 7 population-based cohorts available in the Continental Origins and Genetic Epidemiology Network. In addition to the DARC locus on chromosome 1q23, we identified two other regions (chromosomes 4q13 and 16q22) associated with WBC in African Americans (P<2.5×10(-8)). The lead SNP (rs9131) on chromosome 4q13 is located in the CXCL2 gene, which encodes a chemotactic cytokine for polymorphonuclear leukocytes. Independent evidence of the novel CXCL2 association with WBC was present in 3,551 Hispanic Americans, 14,767 Japanese, and 19,509 European Americans. The index SNP (rs12149261) on chromosome 16q22 associated with WBC count is located in a large inter-chromosomal segmental duplication encompassing part of the hydrocephalus inducing homolog (HYDIN) gene. We demonstrate that the chromosome 16q22 association finding is most likely due to a genotyping artifact as a consequence of sequence similarity between duplicated regions on chromosomes 16q22 and 1q21. Among the WBC loci recently identified in European or Japanese populations, replication was observed in our African-American meta-analysis for rs445 of CDK6 on chromosome 7q21 and rs4065321 of PSMD3-CSF3 region on chromosome 17q21. In summary, the CXCL2, CDK6, and PSMD3-CSF3 regions are associated with WBC count in African American and other populations. We also demonstrate that large inter-chromosomal duplications can

  16. Molecular Epidemiology of Malaria

    PubMed Central

    Conway, David J.

    2007-01-01

    Malaria persists as an undiminished global problem, but the resources available to address it have increased. Many tools for understanding its biology and epidemiology are well developed, with a particular richness of comparative genome sequences. Targeted genetic manipulation is now effectively combined with in vitro culture assays on the most important human parasite, Plasmodium falciparum, and with in vivo analysis of rodent and monkey malaria parasites in their laboratory hosts. Studies of the epidemiology, prevention, and treatment of human malaria have already been influenced by the availability of molecular methods, and analyses of parasite polymorphisms have long had useful and highly informative applications. However, the molecular epidemiology of malaria is currently undergoing its most substantial revolution as a result of the genomic information and technologies that are available in well-resourced centers. It is a challenge for research agendas to face the real needs presented by a disease that largely exists in extremely resource-poor settings, but it is one that there appears to be an increased willingness to undertake. To this end, developments in the molecular epidemiology of malaria are reviewed here, emphasizing aspects that may be current and future priorities. PMID:17223628

  17. Economic burden of smoking in Korea

    PubMed Central

    Kang, H; Kim, H; Park, T; Jee, S; Nam, C; Park, H

    2003-01-01

    Objective: To support tobacco control policies in Korea by providing the estimated annual economic burden attributed to cigarette smoking. Methods: The following two different approaches were used to estimate the cost: "disease specific" and "all causes". In the disease specific approach, we focused on estimating direct and indirect costs involved in treatments of cardiovascular, respiratory, and gastrointestinal diseases, and cancer as a result of smoking, by using an epidemiologic approach—the population attributable risk (PAR). To compute PAR, the relative risks of smoking in terms of physician visits, hospital admission, and death were estimated using the Cox proportional hazard model. In the all causes approach, we examined the differences in direct and indirect costs between smokers and non-smokers for all conditions and types of disease. The major data source was the Korea Medical Insurance Corporation cohort study, which had complete records of smoking status as of 1992 for 115 682 male and 67 932 female insured workers. Results: By the disease specific approach, the estimated costs attributable to smoking in 1998 in Korea ranged from US$2269.42 million ($4.89 million per 100 000 population; 0.59% of gross domestic product (GDP)) to $2956.75 million ($6.37 million; 0.78% of GDP). The all causes approach yielded a minimum cost of $3154.75 million ($6.79 million; 0.82% GDP) and a maximum of $4580.25 million ($9.86 million; 1.19% GDP). Conclusion: The study confirms that smoking places a substantial economic burden on Korean society. In light of this, our study provides evidence for a strong need to develop a national policy to effectively control tobacco consumption in Korea. PMID:12612360

  18. Occupational respiratory cancer in Korea.

    PubMed

    Lee, Hye-Eun; Kim, Hyoung Ryoul

    2010-12-01

    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. PMID:21258597

  19. Gene-Environment Research and Cancer Epidemiology

    Cancer.gov

    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.

  20. South Korea's Economic Development.

    ERIC Educational Resources Information Center

    Ihm, Chon-Sun

    1988-01-01

    Examines South Korea's economic development from being one of the poorest nations in the world in the 1950s to becoming a "rising giant" in international trade. Surveys the path to growth, the reasons for success, and problems and new challenges facing the country as it seeks developed nation status. (GEA)

  1. Dance Education in Korea

    ERIC Educational Resources Information Center

    Byeon, Jae-Kyung

    2012-01-01

    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…

  2. Korea's School Grounds Projects

    ERIC Educational Resources Information Center

    Park, Joohun

    2003-01-01

    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 environments.…

  3. Divided Korea: United Future?

    ERIC Educational Resources Information Center

    Cumings, Bruce

    1995-01-01

    Korea's recorded history extends back before the birth of Christ. Through their long history, the Koreans have endured a variety of social, political, and economical crises. Confucianism has long been one of the most popular religions by which the Korean people have lived. However, Koreans also have embraced Buddhism and Christianity while…

  4. Endodontic Epidemiology

    PubMed Central

    Shahravan, Arash; Haghdoost, Ali Akbar

    2014-01-01

    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

  5. Progress in Malassezia Research in Korea

    PubMed Central

    Kim, Soo Young; Lee, Yang Won; Choe, Yong Beom

    2015-01-01

    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

  6. Progress in Malassezia Research in Korea.

    PubMed

    Kim, Soo Young; Lee, Yang Won; Choe, Yong Beom; Ahn, Kyu Joong

    2015-12-01

    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

  7. Molecular epidemiology of glanders, Pakistan.

    PubMed

    Hornstra, Heidie; Pearson, Talima; Georgia, Shalamar; Liguori, Andrew; Dale, Julia; Price, Erin; O'Neill, Matthew; Deshazer, David; Muhammad, Ghulam; Saqib, Muhammad; Naureen, Abeera; Keim, Paul

    2009-12-01

    We collected epidemiologic and molecular data from Burkholderia mallei isolates from equines in Punjab, Pakistan from 1999 through 2007. We show that recent outbreaks are genetically distinct from available whole genome sequences and that these genotypes are persistent and ubiquitous in Punjab, probably due to human-mediated movement of equines.

  8. Deep Sequencing Reveals the Complete Genome Sequence of Sweet potato virus G from East Timor.

    PubMed

    Maina, Solomon; Edwards, Owain R; Barbetti, Martin J; de Almeida, Luis; Ximenes, Abel; Jones, Roger A C

    2016-01-01

    We present the first complete Sweet potato virus G (SPVG) genome from sweet potato in East Timor and compare it with seven complete SPVG genomes from South Korea (three), Taiwan (two), Argentina (one), and the United States (one). It most resembles the genomes from the United States and South Korea. PMID:27609925

  9. Deep Sequencing Reveals the Complete Genome Sequence of Sweet potato virus G from East Timor

    PubMed Central

    Maina, Solomon; Edwards, Owain R.; Barbetti, Martin J.; de Almeida, Luis; Ximenes, Abel

    2016-01-01

    We present the first complete Sweet potato virus G (SPVG) genome from sweet potato in East Timor and compare it with seven complete SPVG genomes from South Korea (three), Taiwan (two), Argentina (one), and the United States (one). It most resembles the genomes from the United States and South Korea. PMID:27609925

  10. Complete Genome Sequences of the Potyvirus Sweet potato virus 2 from East Timor and Australia

    PubMed Central

    Maina, Solomon; Edwards, Owain R.; de Almeida, Luis; Ximenes, Abel

    2016-01-01

    We present here the first complete genome sequences of Sweet potato virus 2 (SPV2) from sweet potato in Australia and East Timor, and compare these with five complete SPV2 genome sequences from South Korea and one each from Spain and the United States. Both were closely related to SPV2 genomes from South Korea, Spain, and the United States. PMID:27257208

  11. [Field epidemiology and social epidemiology].

    PubMed

    Segura del Pozo, Javier

    2006-01-01

    Comparing field epidemiology and social epidemiology, we pretend to think about the no explicit images and meanings operating in both necessary convergent fields, about the obstacles present in epidemiological practice to fulfil its social function and about the necessity of changing epistemological, methodological and practice grounds, beginning with field epidemiologists teaching programmes. Field epidemiology would tend to act in an absent theoretical frame. On the other hand, social epidemiology would tend to prioritize theoretical developments (thinking and research about social determinants) without correspondent action, because of the limits to change public policies. Other differences are found at intervention level (micro-macrospace), its aim (outbreak control vs. inequalities control) and the way to communicate with society. They are similar in the methodological concern, the predominance of orientation based on positivism and framed through statistic methods, but in process of epistemological opening, the stress experienced between the alternative relationship to a virtual world of data bases or to the real society, their peripherical situation in relation of the political, social, institutional and professional system and the tendency to professional frustration. Finally, we ask ten questions to the field epidemiologists related with their present practice, in order to consider if they are developing social epidemiology, and propose some changes in epidemiologist teaching and practice.

  12. Polygenic Epidemiology

    PubMed Central

    2016-01-01

    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

  13. [Occupational epidemiology].

    PubMed

    Ahrens, W; Behrens, T; Mester, B; Schmeisser, N

    2008-03-01

    The aim of occupational epidemiology is to describe workplace-related diseases and to identify their underlying causes. Its primary goal is to protect workers from hazardous effects of the working process by applying work-related primary and secondary prevention measures. To assess health risks different study designs and a wide array of complex study instruments and methods are frequently employed that cannot be replaced by toxicological investigations. This paper primarily addresses health risks by agent exposures. In this context a central task of occupational epidemiology is careful assessment of exposure. Different data sources, such as work site measurements, register data, archive material, experts' opinion, and the workers' personal estimates of exposure may be used during this process. In addition, biological markers can complement exposure assessment. Since thorough occupational epidemiologic studies allow assessment of disease risks under realistic exposure conditions, their results should be more frequently used to derive workplace-related threshold limit values. PMID:18311483

  14. Polygenic Epidemiology.

    PubMed

    Dudbridge, Frank

    2016-05-01

    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

  15. Understanding aging in Korea.

    PubMed

    Yoon, G; Eun, K

    1995-12-01

    "This study discusses demographic trends, sociocultural characteristics, and policy choices of aging in [South] Korea.... Although the proportion of the elderly was not so high as to worry about aging before 1990, it is projected that one in eight Koreans will be aged 65 or more in 2020. Because the care for the elderly is mostly expected to be provided by each family, not by the state or Korean society, the role of the family is pivotal in coping with [the] aging problem.... Although adult children currently understand that their aged parents need assistance and support from them, they want to solve the issue of support for the elderly in a way different from the traditional.... This paper examines how the changing attitude toward the old is reflected in family life in terms of living arrangement and physical contacts. This paper also describes and discusses the current situation of various welfare policies on the elderly in Korea."

  16. Contig-Layout-Authenticator (CLA): A Combinatorial Approach to Ordering and Scaffolding of Bacterial Contigs for Comparative Genomics and Molecular Epidemiology

    PubMed Central

    Shaik, Sabiha; Kumar, Narender; Lankapalli, Aditya K.; Tiwari, Sumeet K.; Baddam, Ramani; Ahmed, Niyaz

    2016-01-01

    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

  17. Welcome to Korea

    NASA Astrophysics Data System (ADS)

    Park, Youngah

    2009-04-01

    Distinguished Guests and Speakers, Ladies and Gentlemen! On behalf of the Local Organizing Committee, it is my great privilege to welcome all of you to the Third IUPAP International Conference on Women in Physics. Actually, it is quite timely that this Conference is held here in Seoul, Korea, just eight months after our President Lee Myung-bak was inaugurated, because our new President has placed great emphasis on science and technology, particularly basic research.

  18. Cognitive epidemiology

    PubMed Central

    Deary, Ian J; Batty, G David

    2007-01-01

    This glossary provides a guide to some concepts, findings and issues of discussion in the new field of research in which intelligence test scores are associated with mortality and morbidity. Intelligence tests are devised and studied by differential psychologists. Some of the major concepts in differential psychology are explained, especially those regarding cognitive ability testing. Some aspects of IQ (intelligence) tests are described and some of the major tests are outlined. A short guide is given to the main statistical techniques used by differential psychologists in the study of human mental abilities. There is a discussion of common epidemiological concepts in the context of cognitive epidemiology. PMID:17435201

  19. Nutritional Epidemiology

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Although observations on relationships between diet and health have always been recognized—the systematic science of nutritional epidemiology in populations is relatively recent. Important observations propelling the field of nutrition forward were numerous in the 18th and 19th centuries, as it was...

  20. Epidemiological causality.

    PubMed

    Morabia, Alfredo

    2005-01-01

    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.

  1. Hemorrhagic Fever with Renal Syndrome in 4 US Soldiers, South Korea, 2005

    PubMed Central

    Moon, Sung-Sil; Gu, Se Hun; Song, Ki-Joon; Baek, Luck Ju; Kim, Heung Chul; Kijek, Todd; O’Guinn, Monica L.; Lee, John S.; Turell, Michael J.; Klein, Terry A.

    2009-01-01

    Four US soldiers acquired hemorrhagic fever with renal syndrome while training near the Demilitarized Zone, South Korea, in 2005. Hantaan virus sequences were amplified by reverse transcription–PCR from patient serum samples and from lung tissues of striped field mice (Apodemus agrarius) captured at training sites. Epidemiologic investigations specified the ecology of possible sites of patient infection. PMID:19891878

  2. Hemorrhagic fever with renal syndrome in 4 US soldiers, South Korea, 2005.

    PubMed

    Song, Jin Won; Moon, Sung Sil; Gu, Se Hun; Song, Ki Joon; Baek, Luck Ju; Kim, Heung Chul; Kijek, Todd; O'Guinn, Monica L; Lee, John S; Turell, Michael J; Klein, Terry A

    2009-11-01

    Four US soldiers acquired hemorrhagic fever with renal syndrome while training near the Demilitarized Zone, South Korea, in 2005. Hantaan virus sequences were amplified by reverse transcription-PCR from patient serum samples and from lung tissues of striped field mice (Apodemus agrarius) captured at training sites. Epidemiologic investigations specified the ecology of possible sites of patient infection.

  3. Retrospective analysis of whole genome sequencing compared to prospective typing data in further informing the epidemiological investigation of an outbreak of Shigella sonnei in the UK.

    PubMed

    McDonnell, J; Dallman, T; Atkin, S; Turbitt, D A; Connor, T R; Grant, K A; Thomson, N R; Jenkins, C

    2013-12-01

    The aim of this study was to retrospectively assess the value of whole genome sequencing (WGS) compared to conventional typing methods in the investigation and control of an outbreak of Shigella sonnei in the Orthodox Jewish (OJ) community in the UK. The genome sequence analysis showed that the strains implicated in the outbreak formed three phylogenetically distinct clusters. One cluster represented cases associated with recent exposure to a single strain, whereas the other two clusters represented related but distinct strains of S. sonnei circulating in the OJ community across the UK. The WGS data challenged the conclusions drawn during the initial outbreak investigation and allowed cases of dysentery to be implicated or ruled out of the outbreak that were previously misclassified. This study showed that the resolution achieved using WGS would have clearly defined the outbreak, thus facilitating the promotion of infection control measures within local schools and the dissemination of a stronger public health message to the community. PMID:23425681

  4. 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.

    PubMed

    Maglo, Koffi N; Mersha, Tesfaye B; Martin, Lisa J

    2016-01-01

    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

  5. 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

    PubMed Central

    Maglo, Koffi N.; Mersha, Tesfaye B.; Martin, Lisa J.

    2016-01-01

    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

  6. Elementary Teacher Education in Korea.

    ERIC Educational Resources Information Center

    Smith, Douglas C.

    This monograph describes elementary teacher education in South Korea and aspects of Korean society that have contributed to the uniqueness of this educative process. Within the context of comparative education, the essay introduces the cultural, social, and institutional attributes of Korea; discusses specifics of the educative process as a…

  7. North Korea: A Geographical Analysis.

    ERIC Educational Resources Information Center

    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…

  8. Digital Epidemiology

    PubMed Central

    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

    2012-01-01

    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

  9. Epidemiology of Foodborne Norovirus Outbreak in Incheon, Korea

    PubMed Central

    Kim, Na-Yeon; Koh, Yeon-Ja; Lee, Hun-Jae

    2010-01-01

    On June 14, 2008, an outbreak of gastroenteritis occurred among elementary school students in Incheon. We conducted an investigation to identify the source and described the extent of the outbreak. We performed a retrospective cohort study among students, teachers and food handlers exposed to canteen food in the elementary school. Using self-administered questionnaires we collected information on symptoms, days of canteen food eaten, food items consumed. Stool samples were collected from 131 symptomatic people and 11 food handlers. The catering kitchen was inspected and food samples were taken. Of the 1,560 people who ate canteen food, 117 were symptomatic cases, and the attack rate was 7.5%. Consumption of cucumber-crown daisy salad (RR=2.71), fresh cabbage mix (RR=2.23), dried radish salad (RR=3.04) and young radish kimchi (RR=2.52) were associated with illness. Sixty-four (45%) of the 142 stool specimens were positive for Norovirus. Norovirus was detected in 2 food handlers. Interviews with kitchen staff indicated the likelihood of contamination from an infected food handler to the dried radish salad during food processing. The excretion of Norovirus from asymptomatic food handlers may be an infection source of Norovirus outbreaks. PMID:20676321

  10. [Precision medicine: new opportunities and challenges for molecular epidemiology].

    PubMed

    Song, Jing; Hu, Yonghua

    2016-04-01

    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. PMID:27087232

  11. Tobacco control in Korea.

    PubMed

    Park, Kiljun; Kim, Dae Soon; Park, Dong-Jin; Lee, Seon Kui

    2004-01-01

    The Tobacco Business Act and the National Health Promotion Act coexist in Korea, causing conflicts. While the Tobacco Business Act mainly emphasizes the state's financial and economic aspects by describing the operation and control of tobacco business, the National Health Promotion Act states the measures on warnings on the harmful effects of tobacco, prohibition of advertising, and sales limitation for the public's health. In addition to these legal problems, it is not acceptable to continue the Tobacco Business Act, which is completely opposite to the establishment of active social welfare policies for the quality improvement of people's lives. The Tobacco Business Act, whose objective is tobacco business promotion, should be abolished to meet and follow such a desire for health, international trend, and WHO (World Health Organization) FCTC (Framework Convention on Tobacco Control). It would be most proper to ratify the FCTC and abolish the Tobacco Business Act. Also, revision of the National Health Promotion Act is necessary to secure the enforcement and implementation of FCTC in Korea.

  12. Genomic Epidemiology of a Protracted Hospital Outbreak Caused by a Toxin A-Negative Clostridium difficile Sublineage PCR Ribotype 017 Strain in London, England.

    PubMed

    Cairns, M D; Preston, M D; Lawley, T D; Clark, T G; Stabler, R A; Wren, B W

    2015-10-01

    Clostridium difficile remains the leading cause of nosocomial diarrhea worldwide, which is largely considered to be due to the production of two potent toxins: TcdA and TcdB. However, PCR ribotype (RT) 017, one of five clonal lineages of human virulent C. difficile, lacks TcdA expression but causes widespread disease. Whole-genome sequencing was applied to 35 isolates from hospitalized patients with C. difficile infection (CDI) and two environmental ward isolates in London, England. The phylogenetic analysis of single nucleotide polymorphisms (SNPs) revealed a clonal cluster of temporally variable isolates from a single hospital ward at University Hospital Lewisham (UHL) that were distinct from other London hospital isolates. De novo assembled genomes revealed a 49-kbp putative conjugative transposon exclusive to this hospital clonal cluster which would not be revealed by current typing methodologies. This study identified three sublineages of C. difficile RT017 that are circulating in London. Similar to the notorious RT027 lineage, which has caused global outbreaks of CDI since 2001, the lineage of toxin-defective RT017 strains appears to be continually evolving. By utilization of WGS technologies to identify SNPs and the evolution of clonal strains, the transmission of outbreaks caused by near-identical isolates can be retraced and identified.

  13. Genomic Epidemiology of a Protracted Hospital Outbreak Caused by a Toxin A-Negative Clostridium difficile Sublineage PCR Ribotype 017 Strain in London, England.

    PubMed

    Cairns, M D; Preston, M D; Lawley, T D; Clark, T G; Stabler, R A; Wren, B W

    2015-10-01

    Clostridium difficile remains the leading cause of nosocomial diarrhea worldwide, which is largely considered to be due to the production of two potent toxins: TcdA and TcdB. However, PCR ribotype (RT) 017, one of five clonal lineages of human virulent C. difficile, lacks TcdA expression but causes widespread disease. Whole-genome sequencing was applied to 35 isolates from hospitalized patients with C. difficile infection (CDI) and two environmental ward isolates in London, England. The phylogenetic analysis of single nucleotide polymorphisms (SNPs) revealed a clonal cluster of temporally variable isolates from a single hospital ward at University Hospital Lewisham (UHL) that were distinct from other London hospital isolates. De novo assembled genomes revealed a 49-kbp putative conjugative transposon exclusive to this hospital clonal cluster which would not be revealed by current typing methodologies. This study identified three sublineages of C. difficile RT017 that are circulating in London. Similar to the notorious RT027 lineage, which has caused global outbreaks of CDI since 2001, the lineage of toxin-defective RT017 strains appears to be continually evolving. By utilization of WGS technologies to identify SNPs and the evolution of clonal strains, the transmission of outbreaks caused by near-identical isolates can be retraced and identified. PMID:26179308

  14. 15 CFR 746.4 - North Korea.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 15 Commerce and Foreign Trade 2 2013-01-01 2013-01-01 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...

  15. 15 CFR 746.4 - North Korea.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 15 Commerce and Foreign Trade 2 2012-01-01 2012-01-01 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...

  16. Health Inequalities Policy in Korea: Current Status and Future Challenges

    PubMed Central

    Lee, Sang-il

    2012-01-01

    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

  17. Characteristics of Acromegaly in Korea with a Literature Review

    PubMed Central

    Hong, Jae Won; Ku, Cheol Ryong; Kim, Sun Ho

    2013-01-01

    Acromegaly is a slowly progressive disease caused by excessive growth hormone (GH), which is related to a GH secreting pituitary tumor in most cases. Herein, we describe the epidemiology, clinical characteristics, and treatment of acromegaly in Korea with a literature review. The average annual incidence of acromegaly in Korea was 3.9 cases per million people, which was within the range of previous Western studies. The primary treatment for acromegaly was also transsphenoidal adenomectomy, which accounted for 90.4% of patients whose primary therapeutic options were known. The overall surgical remission rates were 89%, 87%, 64%, 70%, and 50% for modified Hardy classification I, II, IIIA, IIIB, and IV, respectively. An updated and larger study regarding the treatment outcome of medical/radiotherapy in Korean acromegalic patients is needed. PMID:24396674

  18. Use of nucleotide sequencing of the genomic cDNA fragments of the capsid/premembrane junction region for molecular epidemiology of dengue type 2 viruses.

    PubMed

    Singh, U B; Seth, P

    2001-06-01

    The recent emergence of dengue hemorrhagic fever/dengue shock syndrome (DHF/ DSS) in India has been a source of concern. In the present study a quantitative comparison of 406 nucleotide long sequence from the capsid-premembrane junction region (C-PrM) of 9 dengue virus type 2 (DEN-2) isolates from Delhi with 10 DEN-2 isolates from diverse geographic areas provided sufficient information for estimating genetic relationships. The data indicated that the 1996 epidemic of DHF in Delhi was caused by genotype IV strains of DEN-2. This genotype, perhaps, displaced genotype V strains of DEN-2, which was circulating genotype in 1967. The period during which this displacement had occurred is not clear from the present study. Nonetheless, similar experience in four countries in Latin America and in Sri Lanka suggest that the introduction of new genotypes of DEN-2 displacing the circulating genotype may be associated with the appearance of DHF/DSS. More work is required to elucidate this hypothesis. Transitions at nucleotide positions 406 and 431 resulted in amino acid substitutions near (aa position 104, methionine --> valine) and at the hinge region (aa position 112, valine --> alanine) of C-PrM, respectively in all/most genotypes of group III and IV DEN-2 viruses analysed. Most of these virus strains have been isolated from DHF/DSS outbreaks. Significance of this observation is discussed. The data presented in this study suggest the utility of C-PrM sequence analysis for molecular epidemiology of dengue viruses.

  19. Further analysis of VNTR and MIRU in the genome of Mycobacterium avium complex, and application to molecular epidemiology of isolates from South America.

    PubMed

    Romano, M I; Amadio, A; Bigi, F; Klepp, L; Etchechoury, I; Llana, M Noto; Morsella, C; Paolicchi, F; Pavlik, I; Bartos, M; Leão, S C; Cataldi, A

    2005-10-31

    All members of Mycobacterium avium complex are serious pathogens for humans and animals. The aim of this study was to look for and analyze VNTR-MIRU loci in the genome of M. avium complex and their preliminary application to test these isolates. In the present study, we identified 22 novel VNTR-MIRU by using Tandem Repeat software: five with a structure similar to MIRU and 17 without MIRU structure; these latter were designated as VNTR. Most VNTR were located within predicted coding regions. Most MIRU were intercistronic with their extremities overlapping the termination and initiation codons of their flanking genes. Some of these VNTR-MIRU exhibited polymorphism among M. avium complex isolates due to insertion or deletion of whole repeats and/or of nucleotide sequence degeneration. We determined the variability of six VNTR-MIRU loci in 21 M. avium subsp. hominissuis and 26 M. avium subsp. paratuberculosis. The analysis identified 15 different alleles with the combination of six VNTR-MIRU in the 21 M. avium subsp. hominissuis with 16 different IS1245 RFLP and four different profiles with PCR-restriction analysis of hsp65 (PRA). However, neither the six VNTR-MIRU loci nor the PRA were able to distinguish M. avium subsp. paratuberculosis isolates with five different IS900 RFLP profiles. In conclusion, some of the VNTR-MIRU loci identified were useful to differentiate M. avium subsp. hominissuis but not M. avium subsp. paratuberculosis isolates here included. However, we observed polymorphism in VNTR-MIRU loci between M. avium subsp. hominissuis and M. avium subsp. paratuberculosis genomes, which could be important in the understanding of the obvious differences in the pathogenic effects of these mycobacteria.

  20. Report from the Maryland epidemiology schizophrenia linkage study: No evidence for linkage between schizophrenia and a number of candidate and other genomic regions using a complex dominant model

    SciTech Connect

    Karayiorgou, M.; Hwang, J.; Elango, R.

    1994-12-15

    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.

  1. Korea's developmental program for superconductivity

    NASA Technical Reports Server (NTRS)

    Hong, Gye-Won; Won, Dong-Yeon; Kuk, Il-Hyun; Park, Jong-Chul

    1995-01-01

    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.

  2. Molecular Epidemiology of Amebiasis

    PubMed Central

    Ali, Ibne Karim M.; Clark, C. Graham; Petri, William A.

    2008-01-01

    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

  3. Korea Research Reactor -1 & 2 Decommissioning Project in Korea

    SciTech Connect

    Park, S. K.; Chung, U. S.; Jung, K. J.; Park, J. H.

    2003-02-24

    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.

  4. Occupational Diseases in Korea

    PubMed Central

    Kim, Eun A

    2010-01-01

    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

  5. Dust Obscures Korea

    NASA Technical Reports Server (NTRS)

    2002-01-01

    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

  6. Genotyping of Mycobacterium tuberculosis: application in epidemiologic studies

    PubMed Central

    Kato-Maeda, Midori; Metcalfe, John Z.; Flores, Laura

    2014-01-01

    Genotyping is used to track specific isolates of Mycobacterium tuberculosis in a community. It has been successfully used in epidemiologic research (termed ‘molecular epidemiology’) to study the transmission dynamics of TB. In this article, we review the genetic markers used in molecular epidemiologic studies including the use of whole-genome sequencing technology. We also review the public health application of molecular epidemiologic tools. PMID:21366420

  7. Teaching about Korea--In Wando and Worland.

    ERIC Educational Resources Information Center

    McGee, Tim; Bellis, David

    2000-01-01

    Stresses three reasons for teaching about Korea and its people in the United States: (1) Korea's potential assistance in solving environmental issues; (2) the role of Korea in promoting world peace; and (3) the economic potential of Korea. Discusses resources for teaching about Korea and provides an appendix with Internet sites on Korea. (CMK)

  8. Serological Detection of Borrelia burgdorferi among Horses in Korea.

    PubMed

    Lee, Seung-Hun; Yun, Sun-Hee; Choi, Eunsang; Park, Yong-Soo; Lee, Sang-Eun; Cho, Gil-Jae; Kwon, Oh-Deog; Kwak, Dongmi

    2016-02-01

    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

  9. Serological Detection of Borrelia burgdorferi among Horses in Korea

    PubMed Central

    Lee, Seung-Hun; Yun, Sun-Hee; Choi, Eunsang; Park, Yong-Soo; Lee, Sang-Eun; Cho, Gil-Jae; Kwon, Oh-Deog; Kwak, Dongmi

    2016-01-01

    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

  10. Genomic DNA extraction from whole blood stored from 15- to 30-years at -20 °C by rapid phenol-chloroform protocol: a useful tool for genetic epidemiology studies.

    PubMed

    Di Pietro, Fabio; Ortenzi, Francesco; Tilio, Martina; Concetti, Fabio; Napolioni, Valerio

    2011-02-01

    Long-term stored (LTS) whole blood collection can be an important source of DNA without collection costs, but there is a lack of information on methods useful to extract genomic DNA from such type of biological material. Here we report a simple and fast revisited phenol/chloroform extraction method from LTS whole blood. Protocol reliability was assessed by comparison with proteinase K and silica-gel membrane spin column-based DNA extraction methods using LTS -20 °C whole blood from 1980, and by testing it on 82 whole blood samples, collected from 1980 to 1995, with high quality (A(260/280) = 1.79 ± 0.32 O.D., A(260/230) = 1.45 ± 0.52 O.D.) and quantity results. Genotyping efficiency was also checked by performing RFLP-PCR and ASP-PCR of p53 Pro72Arg (rs1042522) SNP and hTERT MNS16A VNTR, respectively, resulting in 100% of samples successfully typed. In addition to the goodness and the efficiency of method proposed here, this protocol achieves working time reduction combining extraction and purification steps, allowing to work at room temperature. Furthermore, phenol is able to inactivate any potential nuclease and potential infective sources from the first step on. Based on these results we also conclude that LTS -20 °C whole blood samples may be considered a reliable and potential resource for future genotyping studies and retrospective analysis in a genetic epidemiological setting.

  11. Post-genome-wide association study challenges for lipid traits: describing age as a modifier of gene-lipid associations in the Population Architecture using Genomics and Epidemiology (PAGE) study.

    PubMed

    Dumitrescu, Logan; Carty, Cara L; Franceschini, Nora; Hindorff, Lucia A; Cole, Shelley A; Bůžková, Petra; Schumacher, Fredrick R; Eaton, Charles B; Goodloe, Robert J; Duggan, David J; Haessler, Jeff; Cochran, Barbara; Henderson, Brian E; Cheng, Iona; Johnson, Karen C; Carlson, Chris S; Love, Shelly-Ann; Brown-Gentry, Kristin; Nato, Alejandro Q; Quibrera, Miguel; Anderson, Garnet; Shohet, Ralph V; Ambite, José Luis; Wilkens, Lynne R; Marchand, Loïc Le; Haiman, Christopher A; Buyske, Steven; Kooperberg, Charles; North, Kari E; Fornage, Myriam; Crawford, Dana C

    2013-09-01

    Numerous common genetic variants that influence plasma high-density lipoprotein cholesterol, low-density lipoprotein cholesterol (LDL-C), and triglyceride distributions have been identified via genome-wide association studies (GWAS). However, whether or not these associations are age-dependent has largely been overlooked. We conducted an association study and meta-analysis in more than 22,000 European Americans between 49 previously identified GWAS variants and the three lipid traits, stratified by age (males: <50 or ≥50 years of age; females: pre- or postmenopausal). For each variant, a test of heterogeneity was performed between the two age strata and significant Phet values were used as evidence of age-specific genetic effects. We identified seven associations in females and eight in males that displayed suggestive heterogeneity by age (Phet < 0.05). The association between rs174547 (FADS1) and LDL-C in males displayed the most evidence for heterogeneity between age groups (Phet = 1.74E-03, I(2) = 89.8), with a significant association in older males (P = 1.39E-06) but not younger males (P = 0.99). However, none of the suggestive modifying effects survived adjustment for multiple testing, highlighting the challenges of identifying modifiers of modest SNP-trait associations despite large sample sizes. PMID:23808484

  12. Two chemists in two Koreas.

    PubMed

    Kim, Dong-Won

    2005-03-01

    Taikyu Ree (1902-92) and Seung Ki Li (1905-96) were the most famous and influential scientists in twentieth-century Korea. Trained at Kyoto Imperial University during the Japanese occupation period (1910-45), both followed parallel career paths until 1945 but after that year those paths began to diverge. In 1948 Taikyu Ree moved to the University of Utah where he ran an informal graduate programme to train Korea chemists during the 1950s and 1960s. He became a model scholar in pursuit of knowledge for its own sake. In 1950 Seung Ki Li moved to North Korea where he succeeded in industrialising a new synthetic fibre from polyvinyl alcohol. He became a popular hero who demonstrated the utility of science. His success also helped Kim Il Sung, North Korea dictator, to consolidate his political ideology of Self-Reliance. Despite their different career patterns in very different circumstances, they shared something common; apolitical views and commitment to their work. An investigation of the careers of these two chemists illustrates the interwoven scientific, ideological and economic developments of South and North Korea during the second half of the twentieth century. PMID:16308924

  13. 15 CFR 746.4 - North Korea.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... Democratic People's Republic of Korea (North Korea), except food and medicines classified as EAR99...) Applications to export or reexport humanitarian items (e.g., blankets, basic footwear, heating oil, and...

  14. Special Education in South Korea: Daegu University

    ERIC Educational Resources Information Center

    Kim, Byung Ha; Rhee, Kun Yong; Burns, Carol; Lerner, Janet W.

    2009-01-01

    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…

  15. 76 FR 35740 - North Korea Sanctions Regulations

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-06-20

    ... Office of Foreign Assets Control 31 CFR Part 510 North Korea Sanctions Regulations AGENCY: Office of... Foreign Assets Control (``OFAC'') is amending the North Korea Sanctions Regulations to implement Executive... Control published the North Korea Sanctions Regulations, 31 CFR part 510 (the ``Regulations''),...

  16. Microevolution of Outbreak-Associated Middle East Respiratory Syndrome Coronavirus, South Korea, 2015

    PubMed Central

    Seong, Moon-Woo; Kim, So Yeon; Corman, Victor Max; Kim, Taek Soo; Cho, Sung Im; Kim, Man Jin; Lee, Seung Jun; Lee, Jee-Soo; Seo, Soo Hyun; Ahn, Ji Soo; Yu, Byeong Su; Park, Nare; Oh, Myoung-don; Park, Wan Beom; Lee, Ji Yeon; Kim, Gayeon; Joh, Joon Sung; Jeong, Ina; Kim, Eui Chong

    2016-01-01

    During the 2015 Middle East respiratory syndrome coronavirus outbreak in South Korea, we sequenced full viral genomes of strains isolated from 4 patients early and late during infection. Patients represented at least 4 generations of transmission. We found no evidence of changes in the evolutionary rate and no reason to suspect adaptive changes in viral proteins. PMID:26814649

  17. Health impact assessment in Korea

    SciTech Connect

    Kang, Eunjeong; Lee, Youngsoo; Harris, Patrick; Koh, Kwangwook; Kim, Keonyeop

    2011-07-15

    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.

  18. Agricultural pesticide usage and prioritization in South Korea.

    PubMed

    Cha, Eun Shil; Jeong, Mihye; Lee, Won Jin

    2014-01-01

    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.

  19. Agricultural pesticide usage and prioritization in South Korea.

    PubMed

    Cha, Eun Shil; Jeong, Mihye; Lee, Won Jin

    2014-01-01

    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. PMID:24959760

  20. Acute gastroenteritis outbreaks associated with ground-waterborne norovirus in South Korea during 2008-2012.

    PubMed

    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

    2014-12-01

    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. PMID:24534556

  1. Rural Development in South Korea.

    ERIC Educational Resources Information Center

    Brandt, Vincent S. R.

    1979-01-01

    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…

  2. Inclusive Education in South Korea

    ERIC Educational Resources Information Center

    Kim, Yong-Wook

    2014-01-01

    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…

  3. Fuel Safety Activities in Korea

    SciTech Connect

    Auh, Geun-Sun; Shin, A.D.; Lee, J.S.; Woo, S.W.; Ryu, Y.H.; Kim, Jun-Hwan; Kim, S.K.; Jeong, Y.H.

    2007-07-01

    The current regulatory requirements for fuel performance were based on earlier test data of fresh or low burnup Zircaloy fuels of less than 40 GWD/MTU. Most countries have not changed the current regulatory requirements even if they are actively investigating the high burnup and new cladding alloy effects. Korea agrees with commonly accepted international consensus that although there are technical issues requiring resolutions, these issues do not constitute immediate safety concerns. The high burnup fuel reactor performance experiences of Korea do not show any major problems even if there have been some burnup related fuel failures which are described in the paper. KINS has recommended the industry to have lower fuel failure rates than 1-2 per 50,000 fuel rods. A research project of High Burnup Fuel Safety Tests and Evaluations has started in 2002 under a joint cooperation of KAERI/KNFC/KEPRI and KINS to obtain performance results of high burnup fuel and to develop evaluation technologies of high burnup fuel safety issues. From 1998, KINS has closely monitored and actively participated in international activities such as OECD/NEA CABRI Water Loop Program to reflect on regulatory requirements if needed. KINS will closely monitor the high burnup fuel performances of Korea to strength the regulatory activities if needed. The research activities in Korea including of LOCA and RIA being performed at KAERI with active supports of the industry are summarized in the paper. (authors)

  4. Democratic Citizenship Education in Korea.

    ERIC Educational Resources Information Center

    Eoh, Myung-Ha

    1999-01-01

    Discusses the importance of democratic citizenship education in Korea. Highlights the forces enhancing democratic citizenship education especially the role of the nongovernmental organizations and the Korean Educational Developmental Institute. Considers the various forces inhibiting democratic citizenship education, such as corruption in the…

  5. Life in South Korea Today.

    ERIC Educational Resources Information Center

    Lew, Seok-Choon

    1988-01-01

    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…

  6. Yahak Movement in South Korea

    ERIC Educational Resources Information Center

    Son, Sik

    2004-01-01

    "Yahak" means "night school" in Korean and its history can be traced back to the 1920s when Korea was under Japanese colonial rule. This paper will focus on the yahak movement during the years from 1960 to the 1990s. Yahak played an important role in raising workers' consciousness during this democratic movement. Yahak started as a movement trying…

  7. Korea Earth Observation Satellite Program

    NASA Astrophysics Data System (ADS)

    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

  8. First molecular detection and phylogenetic analysis of Anaplasma phagocytophilum in shelter dogs in Seoul, Korea.

    PubMed

    Lee, Sukyee; Lee, Seung-Hun; VanBik, Dorene; Kim, Neung-Hee; Kim, Kyoo-Tae; Goo, Youn-Kyoung; Rhee, Man Hee; Kwon, Oh-Deog; Kwak, Dongmi

    2016-07-01

    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. PMID:27130537

  9. First molecular detection and phylogenetic analysis of Anaplasma phagocytophilum in shelter dogs in Seoul, Korea.

    PubMed

    Lee, Sukyee; Lee, Seung-Hun; VanBik, Dorene; Kim, Neung-Hee; Kim, Kyoo-Tae; Goo, Youn-Kyoung; Rhee, Man Hee; Kwon, Oh-Deog; Kwak, Dongmi

    2016-07-01

    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.

  10. International Lymphoma Epidemiology Consortium

    Cancer.gov

    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.

  11. Complete Nucleotide Sequence Analysis of the Norovirus GII.4 Sydney Variant in South Korea

    PubMed Central

    Park, Ji-Sun; Lee, Sung-Geun; Cho, Han-Gil; Jheong, Weon-Hwa; Paik, Soon-Young

    2015-01-01

    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. PMID:25688356

  12. Complete nucleotide sequence analysis of the norovirus GII.4 Sydney variant in South Korea.

    PubMed

    Park, Ji-Sun; Lee, Sung-Geun; Jin, Ji-Young; Cho, Han-Gil; Jheong, Weon-Hwa; Paik, Soon-Young

    2015-01-01

    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.

  13. Genetic analysis of duck circovirus in Pekin ducks from South Korea.

    PubMed

    Cha, S-Y; Kang, M; Cho, J-G; Jang, H-K

    2013-11-01

    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.

  14. Occupational Psychiatric Disorders in Korea

    PubMed Central

    Kang, Seong-Kyu

    2010-01-01

    We searched databases and used various online resources to identify and systematically review all articles on occupational psychiatric disorders among Korean workers published in English and Korean before 2009. Three kinds of occupational psychiatric disorders were studied: disorders related to job stress and mental illness, psychiatric symptoms emerging in victims of industrial injuries, and occupational psychiatric disorders compensated by Industrial Accident Compensation Insurance (IACI). Korea does not maintain official statistical records for occupational psychiatric disorders, but several studies have estimated the number of occupational psychiatric disorders using the Korea Workers' Compensation and Welfare Service (COMWEL, formerly KLWC) database. The major compensated occupational psychiatric disorders in Korea were "personality and behavioral disorders due to brain disease, damage, and dysfunction", "other mental disorders due to brain damage and dysfunction and to physical diseases", "reactions to severe stress and adjustment disorders", and "depressive episodes". The most common work-related psychiatric disorders, excluding accidents, were "neurotic, stress-related, and somatoform disorders" followed by "mood disorders". PMID:21258596

  15. Medical waste management in Korea.

    PubMed

    Jang, Yong-Chul; Lee, Cargro; Yoon, Oh-Sub; Kim, Hwidong

    2006-07-01

    The management of medical waste is of great importance due to its potential environmental hazards and public health risks. In the past medical waste was often mixed with municipal solid waste and disposed of in residential waste landfills or improper treatment facilities (e.g. inadequately controlled incinerators) in Korea. In recent years, many efforts have been made by environmental regulatory agencies and waste generators to better manage the waste from healthcare facilities. This paper presents an overview of the current management practices of medical waste in Korea. Information regarding generation, composition, segregation, transportation, and disposal of medical wastes is provided and discussed. Medical waste incineration is identified as the most preferred disposal method and will be the only available treatment option in late 2005. Faced with increased regulations over toxic air emissions (e.g. dioxins and furans), all existing small incineration facilities that do not have air pollution control devices will cease operation in the next few years. Large-scale medical waste incinerators would be responsible for the treatment of medical waste generated by most healthcare facilities in Korea. It is important to point out that there is a great potential to emit air toxic pollutants from such incinerators if improperly operated and managed, because medical waste typically contains a variety of plastic materials such as polyvinyl chloride (PVC). Waste minimization and recycling, control of toxic air emissions at medical waste incinerators, and alternative treatment methods to incineration are regarded to be the major challenges in the future.

  16. 78 FR 66785 - Korea Hydro and Nuclear Power Co., Ltd., and Korea Electric Power Corporation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-11-06

    ... From the Federal Register Online via the Government Publishing Office NUCLEAR REGULATORY COMMISSION Korea Hydro and Nuclear Power Co., Ltd., and Korea Electric Power Corporation AGENCY: Nuclear... APR1400 Standard Plant Design submitted by Korea Hydro and Nuclear Power Co., Ltd. (KHNP) and...

  17. [Future prospects of molecular epidemiology in tuberculosis].

    PubMed

    Matsumoto, Tomoshige; Iwamoto, Tomotada

    2009-12-01

    Before the availability of high-resolution genotyping tools in 1990s, there was a prevailing dogma of little genomic sequence diversity in Mycobacterium tuberculosis. Due to the low levels of genetic variation, it was assumed that M. tuberculosis exhibit very little phenotypic variation in immunologic and virulence factors. The fingerprinting method based on restriction fragment length polymorphisms (RFLP) of IS6110 insertion sequences had unveiled the underestimation of the sequence variation in M. tuberculosis and the importance of strain-to-strain variation for understanding pathogenesis, immune mechanisms, bacterial evolution, and host adaptation. This method became a gold standard for strain differentiation in the molecular epidemiological study. It had lead to a profusion of studies in molecular epidemiology such as the detection of unsuspected transmission, the estimation of the extent of recent transmission, the identification of laboratory cross-contamination, the identification of outbreaks, and distinction between reinfection and relapse. This, in 1990s, is the opening of the molecular epidemiology of tuberculosis. After the completion of genome project of the M. tuberculosis laboratory strain H37Rv, some of the clinical isolates were completely sequenced. This prompted the in silico genome comparison and identified various genomic markers which can give a unifying framework for both epidemiology and evolutionary analysis of M. tuberculosis population. Of them, variable numbers of tandem repeats (VNTR) was found as the most promising PCR-based method which can provide adequate discrimination of M. tuberculosis strains in many cases, including the estimation of M. tuberculosis transmission and the identification of genetic lineages. PCR-based VNTR analysis is easy, rapid, and highly specific and can generate portable digit-based data, unlike the analog information obtained from IS6110 RFLP which is labor intensive. In this regards, investigators can

  18. Genomic diversity of Clostridium difficile strains.

    PubMed

    Janezic, Sandra; Rupnik, Maja

    2015-05-01

    Approaches to exploring Clostridium difficile genomic diversity have ranged from molecular typing methods to use of comparative genome microarrays and whole genome sequence comparisons. The C. difficile population structure is clonal and distributed into six clades, which correlate well with MLST STs (multilocus sequence types) and PCR ribotypes. However, toxigenic strains and strains with increased virulence are distributed throughout several clades. Here we summarize studies on C. difficile genomic diversity, with emphasis on phylogenetic aspects, epidemiological aspect and variability of some virulence factors.

  19. High Toxoplasma gondii Seropositivity among Brain Tumor Patients in Korea

    PubMed Central

    Jung, Bong-Kwang; Song, Hyemi; Kim, Min-Jae; Cho, Jaeeun; Shin, Eun-Hee; Chai, Jong-Yil

    2016-01-01

    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

  20. Draft genome sequence of Virgibacillus halodenitrificans 1806.

    PubMed

    Lee, Sang-Jae; Lee, Yong-Jik; Jeong, Haeyoung; Lee, Sang Jun; Lee, Han-Seung; Pan, Jae-Gu; Kim, Byoung-Chan; Lee, Dong-Woo

    2012-11-01

    Virgibacillus halodenitrificans 1806 is an endospore-forming halophilic bacterium isolated from salterns in Korea. Here, we report the draft genome sequence of V. halodenitrificans 1806, which may reveal the molecular basis of osmoadaptation and insights into carbon and anaerobic metabolism in moderate halophiles. PMID:23105070

  1. Complete Genome Sequences of the Carlavirus Sweet potato chlorotic fleck virus from East Timor and Australia

    PubMed Central

    Maina, Solomon; Edwards, Owain R.; de Almeida, Luis; Ximenes, Abel

    2016-01-01

    We present here the first complete genome sequences of Sweet potato chlorotic fleck virus (SPCFV) from sweet potato in Australia and East Timor, and we compare these with four complete SPCFV genomes from South Korea and one from Uganda. The Australian, East Timorese, South Korean, and Ugandan genomes differed considerably from each other. PMID:27231359

  2. Epidemiology, Genetic Recombination, and Pathogenesis of Coronaviruses.

    PubMed

    Su, Shuo; Wong, Gary; Shi, Weifeng; Liu, Jun; Lai, Alexander C K; Zhou, Jiyong; Liu, Wenjun; Bi, Yuhai; Gao, George F

    2016-06-01

    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.

  3. Epidemiology, Genetic Recombination, and Pathogenesis of Coronaviruses.

    PubMed

    Su, Shuo; Wong, Gary; Shi, Weifeng; Liu, Jun; Lai, Alexander C K; Zhou, Jiyong; Liu, Wenjun; Bi, Yuhai; Gao, George F

    2016-06-01

    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. PMID:27012512

  4. [Epidemiology of Kawasaki disease].

    PubMed

    Nakamura, Yosikazu

    2014-09-01

    Epidemiologic features of Kawasaki disease, in particular in Japan, were summarized. There were three aspects of the epidemiology: (1) frequency(descriptive epidemiology), (2) risk factors(e.g. case-control studies), and (3) natural history(follow-up studies). The nationwide surveys, which was established in 1970, revealed the epidemiologic features of the disease. The number of patients and incidence rate have elevated since mid-1990s. Descriptive features indicates the association between disease onset and both infection and the hosts' factors. A follow-up study over 20 years has been conducted, but it should be continued till all the participants pass away.

  5. International University Will Open in North Korea

    ERIC Educational Resources Information Center

    McNeill, David

    2007-01-01

    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…

  6. Divorce in Korea: Trends and Educational Differentials

    ERIC Educational Resources Information Center

    Park, Hyunjoon; Raymo, James M.

    2013-01-01

    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,…

  7. South Korea Powers Ahead with Globalization Plans

    ERIC Educational Resources Information Center

    McNeill, David

    2009-01-01

    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…

  8. Teaching about Korea in Secondary School.

    ERIC Educational Resources Information Center

    Van Decar, Patricia

    1988-01-01

    Presents 12 study guides for teaching secondary school students about Korean history and culture. The study guides deal with ancient legends, history, family, women's roles, traditions, folk customs, economic development, the division of Korea, the Korean War, links with the United States, and comparisons between North and South Korea. (GEA)

  9. [Molecular epidemiology in the epidemiological transition].

    PubMed

    Tapia-Conyer, R

    1997-01-01

    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. PMID:9504120

  10. Comparative genomic analysis of Staphylococcus aureus FORC_001 and S. aureus MRSA252 reveals the characteristics of antibiotic resistance and virulence factors for human infection.

    PubMed

    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

    2015-01-01

    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.

  11. Occupational Hearing Loss in Korea

    PubMed Central

    2010-01-01

    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

  12. Nutrition policy in South Korea.

    PubMed

    Park, Hye-Kyung

    2008-01-01

    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.

  13. Household Arthropod Allergens in Korea

    PubMed Central

    Jeong, Kyoung Yong

    2009-01-01

    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

  14. Occupational Neurological Disorders in Korea

    PubMed Central

    Kang, Seong-Kyu

    2010-01-01

    The purpose of this article was to provide a literature review of occupational neurological disorders and related research in Korea, focusing on chemical hazards. We reviewed occupational neurological disorders investigated by the Occupational Safety and Health Research Institute of Korean Occupational Safety and Health Agency between 1992 and 2009, categorizing them as neurological disorders of the central nervous system (CNS), of the peripheral nervous system (PNS) or as neurodegenerative disorders. We also examined peer-reviewed journal articles related to neurotoxicology, published from 1984 to 2009. Outbreaks of occupational neurological disorder of the CNS due to inorganic mercury and carbon disulfide poisoning had helped prompt the development of the occupational safety and health system of Korea. Other major neurological disorders of the CNS included methyl bromide intoxication and chronic toxic encephalopathy. Most of the PNS disorders were n-hexane-induced peripheral neuritis, reported from the electronics industry. Reports of manganese-induced Parkinsonism resulted in the introduction of neuroimaging techniques to occupational medicine. Since the late 1990s, the direction of research has been moving toward degenerative disorder and early effect of neurotoxicity. To understand the early effects of neurotoxic chemicals in the preclinical stage, more follow-up studies of a longer duration are necessary. PMID:21258587

  15. Nutrition policy in South Korea.

    PubMed

    Park, Hye-Kyung

    2008-01-01

    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. PMID:18296374

  16. The genomics of mycobacteria.

    PubMed

    Viale, M N; Zumárraga, M J; Araújo, F R; Zarraga, A M; Cataldi, A A; Romano, M I; Bigi, F

    2016-04-01

    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. PMID:27217180

  17. The genomics of mycobacteria.

    PubMed

    Viale, M N; Zumárraga, M J; Araújo, F R; Zarraga, A M; Cataldi, A A; Romano, M I; Bigi, F

    2016-04-01

    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.

  18. Lethal mutagenesis and evolutionary epidemiology.

    PubMed

    Martin, Guillaume; Gandon, Sylvain

    2010-06-27

    The lethal mutagenesis hypothesis states that within-host populations of pathogens can be driven to extinction when the load of deleterious mutations is artificially increased with a mutagen, and becomes too high for the population to be maintained. Although chemical mutagens have been shown to lead to important reductions in viral titres for a wide variety of RNA viruses, the theoretical underpinnings of this process are still not clearly established. A few recent models sought to describe lethal mutagenesis but they often relied on restrictive assumptions. We extend this earlier work in two novel directions. First, we derive the dynamics of the genetic load in a multivariate Gaussian fitness landscape akin to classical quantitative genetics models. This fitness landscape yields a continuous distribution of mutation effects on fitness, ranging from deleterious to beneficial (i.e. compensatory) mutations. We also include an additional class of lethal mutations. Second, we couple this evolutionary model with an epidemiological model accounting for the within-host dynamics of the pathogen. We derive the epidemiological and evolutionary equilibrium of the system. At this equilibrium, the density of the pathogen is expected to decrease linearly with the genomic mutation rate U. We also provide a simple expression for the critical mutation rate leading to extinction. Stochastic simulations show that these predictions are accurate for a broad range of parameter values. As they depend on a small set of measurable epidemiological and evolutionary parameters, we used available information on several viruses to make quantitative and testable predictions on critical mutation rates. In the light of this model, we discuss the feasibility of lethal mutagenesis as an efficient therapeutic strategy.

  19. Vaccine epidemiology: A review

    PubMed Central

    Lahariya, Chandrakant

    2016-01-01

    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

  20. Vaccine epidemiology: A review.

    PubMed

    Lahariya, Chandrakant

    2016-01-01

    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

  1. Full sequence analysis and characterization of a human astrovirus type 1 isolate from South Korea.

    PubMed

    Lee, Sung-Geun; Kang, Lae-Hyung; Jheong, Weon-Hwa; Oh, Mi-Hwa; Lee, Gyu-Cheol; Park, Sujeong; Paik, Soon-Young

    2013-02-01

    Human astroviruses are recognized as an important cause of infantile gastroenteritis around the world. In South Korea, sporadic cases of HAstV infection have been reported since 2002. However, hitherto, there have been no studies reporting the whole genome sequence of an HAstV isolate from South Korea. Hence, we sequenced and analyzed the entire genome of an HAstV-1 strain (lhar) that was isolated in Seoul, South Korea. The whole-genome sequence analysis revealed 3 open reading frames comprising the whole genome: ORF1a (2,763 bp), ORF1b (1,548 bp), and ORF2 (2,364 bp). The lhar strain showed amino acid identities with 8 other reference strains of 87.6-98.7%, 94.2-98.8%, and 62.6-99.0% in the ORF1a, ORF1b, and ORF2 regions, respectively. The amino acid sequence of the capsid region encoded by ORF2 was compared with a total of 19 HAstV-1 strains and 8 HAstVs reference strains isolated in various countries. This revealed 1 amino acid substitution, at aa412 (Pro → Arg) in ORF2. This study, the first to report the full-length sequence of an HAstV isolated in South Korea, is meaningful in that it can be used as a full-length HAstV sequence standard for future comparison studies. It may also prove useful to the field of public health field by facilitating the diagnosis and the prediction of new emerging variants.

  2. Molecular epidemiology of cystic echinococcosis.

    PubMed

    McManus, D P; Thompson, R C A

    2003-01-01

    Echinococcus granulosus exhibits substantial genetic diversity that has important implications for the design and development of vaccines, diagnostic reagents and drugs effective against this parasite. DNA approaches that have been used for accurate identification of these genetic variants are presented here as is a description of their application in molecular epidemiological surveys of cystic echinococcosis in different geographical settings and host assemblages. The recent publication of the complete sequences of the mitochondrial (mt) genomes of the horse and sheep strains of E. granulosus and of E. multilocularis, and the availability of mt DNA sequences for a number of other E. granulosus genotypes, has provided additional genetic information that can be used for more in depth strain characterization and taxonomic studies of these parasites. This very rich sequence information has provided a solid molecular basis, along with a range of different biological, epidemiological, biochemical and other molecular-genetic criteria, for revising the taxonomy of the genus Echinococcus. This has been a controversial issue for some time. Furthermore, the accumulating genetic data may allow insight to several other unresolved questions such as confirming the occurrence and precise nature of the E. granulosus G9 genotype and its reservoir in Poland, whether it is present elsewhere, why the camel strain (G6 genotype) appears to affect humans in certain geographical areas but not others, more precise delineation of the host and geographic ranges of the genotypes characterised to date, and whether additional genotypes of E. granulosus remain to be identified. PMID:15042999

  3. Contemporary Renal Cell Cancer Epidemiology

    PubMed Central

    Chow, Wong-Ho; Devesa, Susan S.

    2010-01-01

    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

  4. Is Multi-Drug Resistant Tuberculosis More Prevalent in HIV-Infected Patients in Korea?

    PubMed

    Lee, Shinwon; Lee, Sun Hee; Mok, Jeong Ha; Lee, Su Jin; Kim, Kye Hyung; Lee, Jeong Eun; Lee, Seung Geun; Chung, Joo Seop; Kwak, Ihm Soo

    2016-11-01

    The epidemiological synergy between human immunodeficiency virus (HIV) and tuberculosis (TB) is a major threat to public health. However, the association between HIV and multi-drug resistant tuberculosis (MDR-TB) is not clear. To explore the association between HIV and MDR-TB infection, a case-control study was performed in Korea. A total of 1606 culture-proven TB patients (45 HIV vs. 1561 non-HIV) from January 2006 to October 2014 were included in this analysis. MDR-TB rates were 11.1% and 8.2% in the HIV and non-HIV groups, respectively (p=0.42), thus indicating that MDR-TB was not significantly associated with HIV infection in Korea. PMID:27593882

  5. Detection of Encephalitozoon spp. from human diarrheal stool and farm soil samples in Korea.

    PubMed

    Kim, Kyungjin; Yoon, Sejoung; Cheun, Hyeng-Il; Kim, Jae-Hwan; Sim, Seobo; Yu, Jae-Ran

    2015-03-01

    Microsporidia are eukaryotic organisms that cause zoonosis and are major opportunistic pathogens in HIV-positive patients. However, there is increasing evidence that these organisms can also cause gastrointestinal and ocular infections in immunocompetent individuals. In Korea, there have been no reports on human infections with microsporidia to date. In the present study, we used real-time PCR and nucleotide sequencing to detect Encephalitozoon intestinalis infection in seven of 139 human diarrheal stool specimens (5%) and Encephalitozoon hellem in three of 34 farm soil samples (8.8%). Genotype analysis of the E. hellem isolates based on the internal transcribed spacer 1 and polar tube protein genes showed that all isolates were genotype 1B. To our knowledge, this is the first report on human E. intestinalis infection in Korea and the first report revealing farm soil samples as a source of E. hellem infection. Because microsporidia are an important public health issue, further large-scale epidemiological studies are warranted.

  6. Surveillance of classical swine fever in wild boar in South Korea from 2010–2014

    PubMed Central

    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

    2015-01-01

    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. PMID:26178821

  7. Surveillance of classical swine fever in wild boar in South Korea from 2010-2014.

    PubMed

    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

    2016-01-01

    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. PMID:26178821

  8. Traditional epidemiology, modern epidemiology, and public health.

    PubMed Central

    Pearce, N

    1996-01-01

    There have been significant developments in epidemiologic methodology during the past century, including changes in basic concepts, methods of data analysis, and methods of exposure measurement. However, the rise of modern epidemiology has been a mixed blessing, and the new paradigm has major shortcomings, both in public health and in scientific terms. The changes in the paradigm have not been neutral but have rather helped change--and have reflected changes in--the way in which epidemiologists think about health and disease. The key issue has been the shift in the level of analysis from the population to the individual. Epidemiology has largely ceased to function as part of a multidisciplinary approach to understanding the causation of disease in populations and has become a set of generic methods for measuring associations of exposure and disease in individuals. This reductionist approach focuses on the individual, blames the victim, and produces interventions that can be harmful. We seem to be using more and more advanced technology to study more and more trivial issues, while the major causes of disease are ignored. Epidemiology must reintegrate itself into public health and must rediscover the population perspective. PMID:8629719

  9. Emergence of decreased susceptibility and resistance to extended-spectrum cephalosporins in Neisseria gonorrhoeae in Korea

    PubMed Central

    Lee, Hyukmin; Unemo, Magnus; Kim, Hyo Jin; Seo, Younghee; Lee, Kyungwon; Chong, Yunsop

    2015-01-01

    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

  10. Recommendations for Carotid Stenting in Korea

    PubMed Central

    Chang, Hyuk Won; Suh, Sang-il; Jeong, Hae Woong; Suh, Dae Chul

    2015-01-01

    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

  11. [Epidemiological research in Brazil].

    PubMed

    Guimarães, R; Lourenço-De-Oliveira, R; Cosac, S

    2001-08-01

    The current epidemiological research in Brazil is described. Secondary data sources were consulted, such as the year 2000 database of the Brazilian Directory of Research Groups and the National Board of Scientific and Technological Development (CNPq). The criterion to identify a group as a research one relies on the existence of at least one research line in the field of epidemiology, as defined by the group leader. After identifying the defined universe of epidemiological research, which included 176 groups and 320 different research lines, the following issues were presented and discussed: the relationships between research financing and health research, focusing on CAPES (Coordination Center for the Advance of University Professionals) graduation programs, public health research and epidemiological research, geographic and institutional distribution and outreach of the current epidemiological research, the researchers and students directly participating in epidemiological research, research topics and patterns of disseminating research findings; the journals where papers in its fullness were published; the financial support of the epidemiological research focusing on the 23 officially recognized graduate programs in public health field. PMID:11600921

  12. Korea`s choice of a new generation of nuclear plants

    SciTech Connect

    Redding, J.R.

    1994-12-31

    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.

  13. Molecular Epidemiology of Influenza A/H3N2 Viruses Circulating in Mexico from 2003 to 2012

    PubMed Central

    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

    2014-01-01

    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

  14. Space Weather Services of Korea

    NASA Astrophysics Data System (ADS)

    Yoon, K.; Hong, S.; Park, S.; Kim, Y. Y.; Wi, G.

    2015-12-01

    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).

  15. Korea tidal power and beyond

    NASA Astrophysics Data System (ADS)

    Song, W. O.; van Walsum, E.

    A study evaluating the tidal power potential on the west coast of Korea is presented. The tidal power plant concept applied to all sites features prefabricated caissons from which the powerhouse and the sluice sections of the plant are built up. In the screening process, all 13 potential sites were compared on the basis of a single basin and single effect schemes operated to produce the maximum amount of energy. The four sites identified as having potential for development (the inner Asan Bay, the outer Asan Bay, the Incheon Bay, and the Garorim Bay) are economically evaluated. It is noted that harbor development and land reclamation can proceed in conjunction with tidal power development.

  16. Space Weather Services of Korea

    NASA Astrophysics Data System (ADS)

    Yoon, KiChang; Kim, Jae-Hun; Kim, Young Yun; Kwon, Yongki; Wi, Gwan-sik

    2016-07-01

    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).

  17. Epidemiology of Crohn's Disease.

    PubMed

    Sandler, R S; Golden, A L

    1986-04-01

    Although our current understanding is limited, epidemiologic investigation of Crohn's disease holds great promise. Certain aspects of the epidemiology are clear. The incidence of Crohn's disease, which has increased over the past few decades, may have reached a plateau. The disease has its peak onset in early life, with a second peak among the elderly. It is more common in the developed countries and among Jews. Whether the disease is related to occupation, social class, marital status, stress, infection, diet, smoking, and oral contraceptives is less certain. This paper reviews the epidemiology of Crohn's disease and proposes areas in which further research is needed.

  18. Evolution and social epidemiology.

    PubMed

    Nishi, Akihiro

    2015-11-01

    Evolutionary biology, which aims to explain the dynamic process of shaping the diversity of life, has not yet significantly affected thinking in social epidemiology. Current challenges in social epidemiology include understanding how social exposures can affect our biology, explaining the dynamics of society and health, and designing better interventions that are mindful of the impact of exposures during critical periods. I review how evolutionary concepts and tools, such as fitness gradient in cultural evolution, evolutionary game theory, and contemporary evolution in cancer, can provide helpful insights regarding social epidemiology.

  19. Moving target: Korea`s nuclear proliferation potential. Working paper No. 5

    SciTech Connect

    Hayes, P.

    1992-10-01

    In early 1992, the nuclear issue was moving so fast in Korea that it bewildered many analysts accustomed to the `glacial` pace of North-South Korean politics since 1953. Korea may spawn a new geopolitical axiom: the longer and harder the freeze, the faster the thaw. This essay seeks to clarify the medium-run trends and possible outcomes that are consistent with this rapidly moving mosaic of events. My purpose is to evaluate the potential for a peaceful resolution of the nuclear dilemma in Korea. First, I outline the basis of Western concern over North Korea`s nuclear activities, and describe the stances taken by the various parties to the Korean conflict on the issue. Next, I analyse the threats emanating from some quarters in Seoul and Washington of attacking North Korea`s nuclear sites-and possible North Korean reprisals. Third, I examine the idea of `challenge inspections` of North Korea`s nuclear program - an alternative that is also discounted as unrealistic. Finally, I sketch a range of possible outcomes of the current impasse, starting with the most optimistic and ending with the most pessimistic (arguably the least likely). None of the key variables underlying these scenarios - the dominant world views in Seoul and Washington, the emphasis on military versus economic power, the ability of the two North Korean elites to achieve mutual understanding - are predetermined. These alternative nuclear futures therefore represent stark choices for, and political challenges to, all parties to the Korean conflict.

  20. Genetic Epidemiology in Aging Research

    PubMed Central

    Matteini, Amy

    2009-01-01

    Over the last two decades, aging research has expanded to include not only age-related disease models, and conversely, longevity and disease-free models, but also focuses on biological mechanisms related to the aging process. By viewing aging on multiple research frontiers, we are rapidly expanding knowledge as a whole and mapping connections between biological processes and particular age-related diseases that emerge. This is perhaps most true in the field of genetics, where variation across individuals has improved our understanding of aging mechanisms, etiology of age-related disease, and prediction of therapeutic responses. A close partnership between gerontologists, epidemiologists, and geneticists is needed to take full advantage of emerging genome information and technology and bring about a new age for biological aging research. Here we review current genetic findings for aging across both disease-specific and aging process domains. We then highlight the limitations of most work to date in terms of study design, genomic information, and trait modeling and focus on emerging technology and future directions that can partner genetic epidemiology and aging research fields to best take advantage of the rapid discoveries in each. PMID:19168782

  1. The dynamic evolution of rheumatology in Korea.

    PubMed

    Kim, Ho-Youn; Song, Yeong-Wook

    2016-03-01

    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.

  2. EPIDEMIOLOGY AND EXPOSURE ASSESSMENT

    EPA Science Inventory

    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...

  3. Epidemiology of varicocele

    PubMed Central

    Alsaikhan, Bader; Alrabeeah, Khalid; Delouya, Guila; Zini, Armand

    2016-01-01

    Varicocele is a common problem in reproductive medicine practice. A varicocele is identified in 15% of healthy men and up to 35% of men with primary infertility. The exact pathophysiology of varicoceles is not very well understood, especially regarding its effect on male infertility. We have conducted a systematic review of studies evaluating the epidemiology of varicocele in the general population and in men presenting with infertility. In this article, we have identified some of the factors that can influence the epidemiological aspects of varicoceles. We also recognize that varicocele epidemiology remains incompletely understood, and there is a need for well-designed, large-scale studies to fully define the epidemiological aspects of this condition. PMID:26763551

  4. Epidemiology of Lice

    ERIC Educational Resources Information Center

    Juranek, Dennis D.

    1977-01-01

    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)

  5. Cancer Epidemiology Cohorts

    Cancer.gov

    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.

  6. A Pediatric Case of Thelaziasis in Korea

    PubMed Central

    Yim, Chung Hyuk; Ko, Jeong Hee; Lee, Jung Hyun; Choi, Yu Mi; Lee, Won Wook; Ahn, Sang Ki; Ahn, Myoung Hee; Choi, Kyong Eun

    2016-01-01

    In the present study, we intended to report a clinical pediatric case of thelaziasis in Korea. In addition, we briefly reviewed the literature on pediatric cases of thelaziasis in Korea. In the present case, 3 whitish, thread-like eye-worms were detected in a 6-year-old-boy living in an urban area and contracted an ocular infection known as thelaziasis incidentally during ecological agritainment. This is the first report of pediatric thelaziasis in Seoul after 1995. PMID:27417087

  7. Genome sequence of Xanthomonas axonopodis pv. punicae strain LMG 859.

    PubMed

    Sharma, Vikas; Midha, Samriti; Ranjan, Manish; Pinnaka, Anil Kumar; Patil, Prabhu B

    2012-05-01

    We report the 4.94-Mb genome sequence of Xanthomonas axonopodis pv. punicae strain LMG 859, the causal agent of bacterial leaf blight disease in pomegranate. The draft genome will aid in comparative genomics, epidemiological studies, and quarantine of this devastating phytopathogen. PMID:22493202

  8. Draft Genome Sequence of Leptolyngbya sp. KIOST-1, a Filamentous Cyanobacterium with Biotechnological Potential for Alimentary Purposes

    PubMed Central

    Kim, Ji Hyung

    2016-01-01

    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

  9. Draft Genome Sequence of Leptolyngbya sp. KIOST-1, a Filamentous Cyanobacterium with Biotechnological Potential for Alimentary Purposes.

    PubMed

    Kim, Ji Hyung; Kang, Do-Hyung

    2016-01-01

    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

  10. [Molecular and genetic epidemiology].

    PubMed

    Kang, D H

    2001-04-21

    Molecular epidemiology is defined as "the use of biological markers in epidemiologic research" and genetic epidemiology is defined as "the study of the interaction between genetic and environmental factors in epidemiologic research". Traditional epidemiologic approaches defined as "the study of the distribution and determinants of disease frequency in human population" could not address the importance of genetic susceptibility of humans in disease occurrence. However, the use of biological or genetic markers identified and characterized by the help of advance in molecular biology and human genetics now can provide us better understanding of multi-factorial or multistep disease occurrence in humans. Biological markers used in molecular epidemiology are classified into three groups: biomarkers of exposure (i.e., carcinogen metabolites in human urine, DNA-adducts, etc.), biomarkers of effects (i.e., oncoproteins, tumor markers, etc.), and biomarkers of susceptibility (i.e., genetic polymorphisms of carcinogen metabolism enzymes, DNA repair, etc.). Susceptibility genes involved in disease pathogenesis are categorized into two groups: high penetrance genes (i.e., BRAC1, RB, etc.) and low penetrance genes (i.e., GSTs, XRCC1, etc.). This paper will address the usefulnesses of bomarkers in edpidemiologic research and will show the examples of the use of selected low penetrance genes involved in human carcinogenesis. The importance of multidisciplinary approaches among epidemiologists, molecular biologists, and human geneticists will also be discussed.

  11. Incidence and Survival of Childhood Cancer in Korea

    PubMed Central

    Park, Hyeon Jin; Moon, Eun-Kyeong; Yoon, Ju Young; Oh, Chang-Mo; Jung, Kyu-Won; Park, Byung Kiu; Shin, Hee Young; Won, Young-Joo

    2016-01-01

    Purpose An epidemiologic study of childhood cancer would provide useful information on cancer etiology and development of management guidelines. Materials and Methods Data from the Korea National Cancer Incidence Database were used to examine the incidence and survival of cancer in patients aged 0-14 years. Patients were grouped according to the International Classification of Childhood Cancer, 3rd edition. Age-specific and age-standardized incidences per million and estimated annual percentage change (APC) were calculated by sex and age. Five-year relative survival was calculated for four periods from 1993 to 2011. Results The study comprised 15,113 patients with malignant neoplasms. Age-standardized incidence rates for all cancers were 134.9 per million children in 1999-2011 and 144.0 and 124.9 per million for males and females, respectively (M/F ratio, 1.2; p < 0.05). The highest incidences were observed for ‘leukemias, myeloproliferative diseases, and myelodysplastic diseases’ (group I) (46.4), ‘central nervous system neoplasms’ (group III) (18.3), and ‘lymphomas and reticuloendothelial neoplasms’ (group II) (13.4). Age-standardized incidence increased from 117.9 in 1999 to 155.3 in 2011, with an APC of 2.4% (95% confidence interval, 2.1 to 2.7). There was a significant increase of APC in ‘neuroblastoma and other peripheral nervous cell tumors’ (group IV) (5.6%) and ‘other malignant epithelial neoplasms and malignant melanomas’ (group XI) (5.6%). The 5-year relative survival rate for all childhood cancers improved significantly from 56.2% (1993-1995) to 78.2% (2007-2011) (males, 56.7% to 77.7%; females, 55.5% to 78.8%). Conclusion This study provides reliable information on incidence and survival trends for childhood cancer in Korea. PMID:26790965

  12. Urbanization of Scrub Typhus Disease in South Korea

    PubMed Central

    Park, Sang-Won; Ha, Na-Young; Ryu, Boyeong; Bang, Ji Hwan; Song, Hoyeon; Kim, Yuri; Kim, Gwanghun; Oh, Myoung-don; Cho, Nam-Hyuk; Lee, Jong-koo

    2015-01-01

    Background Scrub typhus is an endemic disease in Asia. It has been a rural disease, but indigenous urban cases have been observed in Seoul, South Korea. Urban scrub typhus may have a significant impact because of the large population. Methods Indigenous urban scrub typhus was epidemiologically identified in Seoul, the largest metropolitan city in South Korea, using national notifiable disease data from 2010 to 2013. For detailed analysis of clinical features, patients from one hospital that reported the majority of cases were selected and compared to a historic control group. Chigger mites were prospectively collected in the city using a direct chigger mite-collecting trap, and identified using both phenotypic and 18S rDNA sequencing analyses. Their infection with Orientia tsutsugamushi was confirmed by sequencing the 56-kDa antigen gene. Results Eighty-eight cases of urban scrub typhus were determined in Seoul. The possible sites of infection were mountainous areas (56.8%), city parks (20.5%), the vicinity of one’s own residence (17.0%), and riversides (5.7%). Eighty-seven chigger mites were collected in Gwanak mountain, one of the suspected infection sites in southern Seoul, and seventy-six (87.4%) of them were identified as Helenicula miyagawai and eight (9.2%) as Leptotrombidium scutellare. Pooled DNA extracted from H. miyagawai mites yielded O. tsutsugamushi Boryong strain. Twenty-six patients from one hospital showed low APACHE II score (3.4 ± 2.7), low complication rate (3.8%), and no hypokalemia. Conclusions We identified the presence of indigenous urban scrub typhus in Seoul, and a subgroup of them had mild clinical features. The chigger mite H. miyagawai infected with O. tsutsugamushi within the city was found. In endemic area, urban scrub typhus needs to be considered as one of the differential febrile diseases and a target for prevention. PMID:26000454

  13. Evolution, phylogeny, and molecular epidemiology of Chlamydia.

    PubMed

    Nunes, Alexandra; Gomes, João P

    2014-04-01

    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.

  14. The Diabetes Epidemic in Korea

    PubMed Central

    2016-01-01

    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

  15. A systematic review of genetic diversity of human rotavirus circulating in South Korea.

    PubMed

    Than, Van Thai; Jeong, Sunyoung; Kim, Wonyong

    2014-12-01

    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[8], followed by G3P[8], G4P[6], and G2P[4], accounted for approximately 76.7% of the total identified strains, and more recently, rotavirus G9P[8] 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.

  16. Bibliometric investigation on preventive medicine in North Korea: a coauthor and keyword network analysis.

    PubMed

    Jung, Minsoo

    2013-01-01

    This study examined the 2 preventive medicine journals in North Korea by using coauthor and keyword network analysis on the basis of medical informatics and bibliometrics. Used were the Journal of Chosun Medicine (JCM) and the Journal of Preventive Medicine (JPM) (from the first volume of 1997 to the fourth volume of 2006) as data. Extracted were 1734 coauthors from 1104 articles and 1567 coauthors from 1172 articles, respectively. Huge single components were extracted in the coauthor analysis, which indicated a tendency toward structuralization. However, the 2 journals differed in that JPM showed a relative tendency toward specialization, whereas JCM showed one toward generalization. Seventeen and 33 keywords were extracted from each journal in the keyword analysis; JCM mainly concerned pathological research, whereas JPM mainly concerned virus and basic medicine studies that were based on infection and immunity. In contrast to South Korea, North Korea has developed Juche medicine, which came from self-reliance ideology and gratuitous medical service. According to the present study, their ideology was embodied by the discovery of bacteria, study on immune system, and emphasis on pathology, on the basis of experimental epidemiology. However, insufficient research has been conducted thus far on population health and its related determinants.

  17. Shifting epidemiology of Flaviviridae.

    PubMed

    Petersen, Lyle R; Marfin, Anthony A

    2005-04-01

    The dengue, West Nile, Japanese encephalitis and yellow fever viruses are important mosquito-borne viruses whose epidemiology is shifting in response to changing societal factors, such as increasing commerce, urbanization of rural areas, and population growth. All four viruses are expanding geographically, as exemplified by the emergence of West Nile virus in the Americas and Japanese encephalitis virus in Australasia. The large, recent global outbreaks of severe neurological disease caused by West Nile virus, the increasing frequency of dengue hemorrhagic fever outbreaks in the Americas, and the emergence of yellow fever virus vaccination-associated viscerotropic disease, are new clinical epidemiologic trends. These worrisome epidemiologic trends will probably continue in coming decades, as a reversal of their societal and biological drivers is not in sight. Nevertheless, the substantial reductions in Japanese encephalitis virus incidence resulting from vaccination programs and economic development in some Asian countries provide some encouragement within this overall guarded outlook.

  18. Whose epidemiology, whose health?

    PubMed

    Wing, S

    1998-01-01

    Simplistic claims about the objectivity of science have been challenged from a variety of perspectives. Evaluation of the external context of production of knowledge and the methodological approaches to posing questions and assembling evidence shows that there is no pure "science"; rather, all scientific knowledge is shaped by the social history of its production. Examples are given of how quantitative concepts in modern epidemiology influence the recognition of the causes of disease. The author uses the phenomenon of intensive swine production by vertically integrated agribusiness to illustrate how broad problems such as environmental racism, agricultural determinants of nutrition, loss of natural resources, and conditions conducive to emergence of new diseases are hidden by epidemiological approaches that fit into corporate policy perspectives. It is critically important to ask who produces epidemiological knowledge, and whose health is promoted by that knowledge.

  19. Genetic epidemiology, genetic maps and positional cloning.

    PubMed Central

    Morton, Newton E

    2003-01-01

    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

  20. Seismic noise level variation in South Korea

    NASA Astrophysics Data System (ADS)

    Sheen, D.; Shin, J.

    2008-12-01

    The variations of seismic background noise in South Korea have been investigated by means of power spectral analysis. The Korea Institute of Geoscience and Mineral Resources (KIGAM) and the Korea Meteorological Administation (KMA) have national wide seismic networks in South Korea, and, in the end of 2007, there are 30 broadband stations which have been operating for more than a year. In this study, we have estimated the power spectral density of seismic noise for 30 broadband stations from 2005 to 2007. Since we estimate PSDs from a large dataset of continuous waveform in this study, a robust PSD estimate of McNamara and Buland (2004) is used. In the frequency range 1-5 Hz, the diurnal variations of noise are observed at most of stations, which are especially larger at coastal stations and at insular than at inland. Some stations shows daily difference of diurnal variations, which represents that cultural activities contribute to the noise level of a station. The variation of number of triggered stations, however, shows that cultural noise has little influence on the detection capability of seismic network in South Korea. Seasonal variations are observed well in the range 0.1-0.5 Hz, while much less found in the frequency range 1-5 Hz. We observed that strong peaks in the range 0.1-0.5 Hz occur at the summer when Pacific typhoons are close to the Korean Peninsula.

  1. Asbestos exposure and malignant mesothelioma in Korea.

    PubMed

    Lee, Kyoung-Ho; Yoon, Hyung-Suk; Choi, Sang-Jun; Kang, Daehee

    2009-01-01

    Although importation of asbestos to Korea has decreased, there are growing concerns of its hazardous effects. This paper describes the use and occupational exposure to asbestos, and the incidence and mortality of malignant mesotheliomas in Korea. Asbestos raw material imports from other countries peaked between 1990 and 1995, but importation of asbestos-containing and -processed materials has steadily increased until now. A comprehensive exposure survey was conducted in Korea between 1995 and 2006. The average airborne asbestos concentration was lower than from other countries and steadily decreased during the study period. The number of malignant mesothelioma cases in Korea was 48 in 1998, 39 in 1999, 45 in 2000, 38 in 2001, and 46 in 2002. There were 334 deaths due to malignant mesothelioma and an average of 30.4 deaths per year between 1996 and 2006. The number of deaths attributed to malignant mesothelioma ranged from 16 cases in 1999 to 57 cases in 2006. The magnitude of asbestos-related health problems in Korea has been underestimated due to under-diagnosis, incomplete reports, and shorter duration of exposure. A nationwide surveillance system for asbestos exposure and malignant mesothelioma should therefore be implemented.

  2. Epidemiology of Lung Cancer.

    PubMed

    Mao, Yousheng; Yang, Ding; He, Jie; Krasna, Mark J

    2016-07-01

    Lung cancer has been transformed from a rare disease into a global problem and public health issue. The etiologic factors of lung cancer become more complex along with industrialization, urbanization, and environmental pollution around the world. Currently, the control of lung cancer has attracted worldwide attention. Studies on the epidemiologic characteristics of lung cancer and its relative risk factors have played an important role in the tertiary prevention of lung cancer and in exploring new ways of diagnosis and treatment. This article reviews the current evolution of the epidemiology of lung cancer. PMID:27261907

  3. Development of Source-Receptor matrix over South Korea in support of GAINS-Korea model

    NASA Astrophysics Data System (ADS)

    Choi, K. C.; Woo, J. H.; Kim, H. K.; Lee, Y. M.; Kim, Y.; Heyes, C.; Lee, J. B.; Song, C. K.; Han, J.

    2014-12-01

    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.

  4. Assessment of the risk posed to Singapore by the 2015 Middle East respiratory syndrome outbreak in the Republic of Korea

    PubMed Central

    Zhang, Emma Xuxiao; Oh, Olivia Seen Huey; See, Wanhan; Raj, Pream; James, Lyn; Khan, Kamran

    2016-01-01

    Objective To assess the public health risk to Singapore posed by the Middle East respiratory syndrome (MERS) outbreak in the Republic of Korea in 2015. Methods The likelihood of importation of MERS cases and the magnitude of the public health impact in Singapore were assessed to determine overall risk. Literature on the epidemiology and contextual factors associated with MERS coronavirus infection was collected and reviewed. Connectivity between the Republic of Korea and Singapore was analysed. Public health measures implemented by the two countries were reviewed. Results The epidemiology of the 2015 MERS outbreak in the Republic of Korea remained similar to the MERS outbreaks in Saudi Arabia. In addition, strong infection control and response measures were effective in controlling the outbreak. In view of the air traffic between Singapore and MERS-affected areas, importation of MERS cases into Singapore is possible. Nonetheless, the risk of a serious public health impact to Singapore in the event of an imported case of MERS would be mitigated by its strong health-care system and established infection control practices. Discussion The MERS outbreak was sparked by an exported case from the Middle East, which remains a concern as the reservoir of infection (thought to be camels) continues to exist in the Middle East, and sporadic cases in the community and outbreaks in health-care settings continue to occur there. This risk assessment highlights the need for Singapore to stay vigilant and to continue enhancing core public health capacities to detect and respond to MERS coronavirus. PMID:27508087

  5. Recent meteorite falls in South Korea

    NASA Astrophysics Data System (ADS)

    Choi, Y.; Kim, M.; Byun, Y.; Yi, H.; Chang, S.; Choi, J.; Sohn, J.; Moon, H.; Park, J.

    2014-07-01

    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.

  6. 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).

    PubMed

    Woo, Hye Won; Choi, Bo Youl; Kim, Mi Kyung

    2016-01-01

    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

  7. 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)

    PubMed Central

    Woo, Hye Won; Choi, Bo Youl; Kim, Mi Kyung

    2016-01-01

    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

  8. Korea: Balancing Economic Growth and Social Protection for Older Adults

    ERIC Educational Resources Information Center

    Yoon, Hyun-Sook

    2013-01-01

    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.…

  9. English Immersion and Educational Inequality in South Korea

    ERIC Educational Resources Information Center

    Jeon, Mihyon

    2012-01-01

    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…

  10. Brain Korea 21 Phase II: A New Evaluation Model. Monograph

    ERIC Educational Resources Information Center

    Seong, Somi; Popper, Steven W.; Goldman, Charles A.; Evans, David K.

    2008-01-01

    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…

  11. 75 FR 53711 - Polyethylene Terephthalate (PET) Film From Korea

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-09-01

    ... Department of Commerce (Commerce) issued an antidumping duty order on imports of PET film from Korea (56 FR..., Commerce issued a continuation of the antidumping duty order on imports of PET film from Korea (65 FR 11984... issued a continuation of the antidumping duty order on imports of PET film from Korea (70 FR 61118)....

  12. Comparison of incubation period distribution of human infections with MERS-CoV in South Korea and Saudi Arabia

    PubMed Central

    Virlogeux, Victor; Fang, Vicky J.; Park, Minah; Wu, Joseph T.; Cowling, Benjamin J.

    2016-01-01

    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

  13. The characteristics of emergency department presentations related to acute herbicide or insecticide poisoning in South Korea between 2011 and 2014.

    PubMed

    Moon, Jeong Mi; Chun, Byeong Jo; Cho, Yong Soo

    2016-01-01

    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. PMID:27267557

  14. Genome-wide Association Studies from the Cancer Genetic Markers of Susceptibility (CGEMS) Initiative | Office of Cancer Genomics

    Cancer.gov

    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.

  15. Phylogenetically resolving epidemiologic linkage

    DOE PAGESBeta

    Romero-Severson, Ethan O.; Bulla, Ingo; Leitner, Thomas

    2016-02-22

    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

  16. Causality in epidemiology.

    PubMed

    Kamangar, Farin

    2012-10-01

    This article provides an introduction to the meaning of causality in epidemiology and methods that epidemiologists use to distinguish causal associations from non-causal ones. Alternatives to causal association are discussed in detail. Hill's guidelines, set forth approximately 50 years ago, and more recent developments are reviewed. The role of religious and philosophic views in our understanding of causality is briefly discussed.

  17. Epidemiology of Down Syndrome

    ERIC Educational Resources Information Center

    Sherman, Stephanie L.; Allen, Emily G.; Bean, Lora H.; Freeman, Sallie B.

    2007-01-01

    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…

  18. Phylogenetically resolving epidemiologic linkage.

    PubMed

    Romero-Severson, Ethan O; Bulla, Ingo; Leitner, Thomas

    2016-03-01

    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

  19. Phylogenetically resolving epidemiologic linkage

    PubMed Central

    Romero-Severson, Ethan O.; Bulla, Ingo; Leitner, Thomas

    2016-01-01

    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

  20. [Toxoplasmosis: Epidemiology, Diagnosis, Treatment].

    PubMed

    Khryanin, A A; Reshetnikov, O V; Kuvshinova, I N

    2015-01-01

    The up-to-date literature and original data on the epidemiology, diagnosis and treatment of toxoplasmosis are presented. Particular attention is paid to the parasite infection during pregnancy. Spiramycin is the drug of choice for acute toxoplasmosis in pregnant women.

  1. Epidemiology of Cardiovascular Diseases.

    ERIC Educational Resources Information Center

    Jenkins, C. David

    1988-01-01

    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…

  2. Practical Treatments for Constipation in Korea

    PubMed Central

    Park, Kyung-Sik; Park, Moo-In; Shin, Jeong-Eun; Jung, Kee-Wook; Kim, Seong-Eun; Lee, Tae-Hee; Koo, Hoon-Sup

    2012-01-01

    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

  3. Systemic Analysis of Foodborne Disease Outbreak in Korea.

    PubMed

    Lee, Jong-Kyung; Kwak, No-Seong; Kim, Hyun Jung

    2016-02-01

    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. PMID:26863429

  4. Cancers of the upper aerodigestive tract in Korea.

    PubMed Central

    Cho, Kyung Ja; Khang, Shin Kwang; Lee, Seung Sook; Koh, Jae Soo; Chung, Jin Haeng; Lee, Yong Sik; Shim, Yoon Sang

    2002-01-01

    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

  5. Genomic diversity of Clostridium difficile strains.

    PubMed

    Janezic, Sandra; Rupnik, Maja

    2015-05-01

    Approaches to exploring Clostridium difficile genomic diversity have ranged from molecular typing methods to use of comparative genome microarrays and whole genome sequence comparisons. The C. difficile population structure is clonal and distributed into six clades, which correlate well with MLST STs (multilocus sequence types) and PCR ribotypes. However, toxigenic strains and strains with increased virulence are distributed throughout several clades. Here we summarize studies on C. difficile genomic diversity, with emphasis on phylogenetic aspects, epidemiological aspect and variability of some virulence factors. PMID:25700631

  6. RNA virus genomics: a world of possibilities

    PubMed Central

    Holmes, Edward C.

    2009-01-01

    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

  7. Adolescent's sexual problems in Korea.

    PubMed

    Kang, B S

    1990-07-01

    This article discusses primary contributors of sexual problems among Korean adolescents. As a result of improved nutrition, physical maturity is occurring at an earlier age in Korean youths. On the other hand, marital age has increased; the average age for males to marry is 27.3 years and 24.1 years in females. Hence, these factors extend the time frame between onset of sexual maturity and marriage. Enrollment in schools has risen; middle school registration has increased from 74.2% in 1975 to 99.7% in 1985 and from 43.6% to 78.3% in high schools. Increased enrollment has also been observed at the university level which may promote prolonged educational periods; this focus on education may reduce sexual interest among students. Improved employment opportunities may also influence sexual behavior among adolescents; urban migration can encourage casual relationships. Changes in family structure and sexual morals has promoted liberal attitudes regarding sexual practices. Increased exposure to mass media has affected adolescent sexual problems; 99.1% of the households in 1985 possessed televisions. These sexual problems include onset of sexual intercourse at an earlier age, unwanted pregnancies, increased induced abortions, and early childbirth. Overall, sexual activity in females has risen from 3.6% in 1965 to 14.5% in 1981 and from 18.5% in 1971 for males to 27.7% in 1981. Pre-marital pregnancy rates have continually increased since 1950; this has resulted in a rise of unwed mothers' consultations which reflects adolescent childbirths. Sex-related crime have also increased; rape ranks 3rd in crimes committed by Korean youth. Sex education and family planning should be provided for adolescents. Furthermore, counseling services should be available to youth regarding unwanted pregnancies, sexually transmitted diseases, and contraception. The Planned Parenthood Federation of Korea provides youth sex telephone services in which adolescents can acquire information on

  8. Adolescent's sexual problems in Korea.

    PubMed

    Kang, B S

    1990-07-01

    This article discusses primary contributors of sexual problems among Korean adolescents. As a result of improved nutrition, physical maturity is occurring at an earlier age in Korean youths. On the other hand, marital age has increased; the average age for males to marry is 27.3 years and 24.1 years in females. Hence, these factors extend the time frame between onset of sexual maturity and marriage. Enrollment in schools has risen; middle school registration has increased from 74.2% in 1975 to 99.7% in 1985 and from 43.6% to 78.3% in high schools. Increased enrollment has also been observed at the university level which may promote prolonged educational periods; this focus on education may reduce sexual interest among students. Improved employment opportunities may also influence sexual behavior among adolescents; urban migration can encourage casual relationships. Changes in family structure and sexual morals has promoted liberal attitudes regarding sexual practices. Increased exposure to mass media has affected adolescent sexual problems; 99.1% of the households in 1985 possessed televisions. These sexual problems include onset of sexual intercourse at an earlier age, unwanted pregnancies, increased induced abortions, and early childbirth. Overall, sexual activity in females has risen from 3.6% in 1965 to 14.5% in 1981 and from 18.5% in 1971 for males to 27.7% in 1981. Pre-marital pregnancy rates have continually increased since 1950; this has resulted in a rise of unwed mothers' consultations which reflects adolescent childbirths. Sex-related crime have also increased; rape ranks 3rd in crimes committed by Korean youth. Sex education and family planning should be provided for adolescents. Furthermore, counseling services should be available to youth regarding unwanted pregnancies, sexually transmitted diseases, and contraception. The Planned Parenthood Federation of Korea provides youth sex telephone services in which adolescents can acquire information on

  9. Molecular Epidemiology of Foodborne Pathogens

    NASA Astrophysics Data System (ADS)

    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".

  10. Crisis and Employment: The Case of Korea

    ERIC Educational Resources Information Center

    Cho, Dongchul; Shin, Sukha

    2012-01-01

    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…

  11. Korea targets leadership role in physics

    NASA Astrophysics Data System (ADS)

    Durrani, Matin

    2013-11-01

    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.

  12. Genetic diversity of Lycoris endemic to Korea

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Extensive taxonomic relationships among Lycoris Herb. (Amaryllidaceae) taxa native to Korea have not been analyzed previously. This study was carried out to investigate the hybrid origin, genetic diversity, and relationships of Lycoris taxa (L. flavescens, L. uydoensis, L. chejuensis, L. chinensis ...

  13. [[Prevalence of induced abortion in Korea

    PubMed

    Lim, J; Lee, S; Bae, H

    1989-07-01

    The authors analyze recent trends in the prevalence of induced abortions in South Korea. They attempt to determine motivations for abortion, examine its side effects, and investigate the impact of induced abortions on infertility. The focus is on creating recommendations for population policy and maternal and child health care. Data are from the 1988 Korean National Fertility and Family Health Survey. (SUMMARY IN ENG)

  14. The Quality of Life in South Korea

    ERIC Educational Resources Information Center

    Park, Chong-Min

    2009-01-01

    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…

  15. Collaborative Reasoning in China and Korea

    ERIC Educational Resources Information Center

    Dong, Ting; Anderson, Richard C.; Kim, Il-Hee; Li, Yuan

    2008-01-01

    Students at two sites in China and one site in Korea engaged in Collaborative Reasoning, an approach to discussion that requires self-management, free participation, and critical thinking. The discontinuity between the usual adult-dominated discourse of Chinese and Korean homes and classrooms and the expected discourse of Collaborative Reasoning…

  16. English Textbooks in Japan and Korea

    ERIC Educational Resources Information Center

    Yuasa, Katsura

    2010-01-01

    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…

  17. Country Profiles, The Republic of Korea.

    ERIC Educational Resources Information Center

    Han, Dae Woo; And Others

    A profile of the Republic of Korea is sketched in this paper. Emphasis is placed on the nature, scope, and accomplishments of population activities in the country. Topics and sub-topics include: location and description of the country; population (size, growth patterns, age structure, urban/rural distribution, ethnic and religious composition,…

  18. [Epidemiological situation of Chad].

    PubMed

    Korzeniewski, Krzysztof

    2008-10-01

    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.

  19. Epidemiology and moral philosophy.

    PubMed Central

    Westrin, C G; Nilstun, T; Smedby, B; Haglund, B

    1992-01-01

    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

  20. Dengue: update on epidemiology.

    PubMed

    Wilson, Mary Elizabeth; Chen, Lin H

    2015-01-01

    The epidemiology of dengue fever has undergone major shifts in recent decades. The global distribution has expanded to include more geographic areas. The intensity of transmission and the severity of infections have increased in areas where infection was already endemic. Multiple studies provide a clearer picture of the epidemiology and allow mapping of its distribution and change over time. Despite major efforts to control transmission, competent vectors now infest most tropical and subtropical regions; Aedes albopictus, also a competent vector, is able to survive in temperate areas, placing parts of Europe and North America at risk for local transmission. Many research teams in dengue-endemic areas are working to identify key local weather, vector, and other variables that would allow prediction of a likely epidemic early enough to permit interventions to avert it or blunt its impact.

  1. Epidemiology of colorectal cancer

    PubMed Central

    Marley, Andrew R; Nan, Hongmei

    2016-01-01

    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

  2. The prevalence and risk factors for pterygium in South Korea: the Korea National Health and Nutrition Examination Survey (KNHANES) 2009-2010

    PubMed Central

    Mun, Gui Hyeong

    2016-01-01

    OBJECTIVES To determine the prevalence and risk factors for pterygium in the adult Korean population of South Korea. METHODS Data were analyzed from 9,193 participants who were 40 years of age or older from the Korea National Health and Nutrition Examination Survey (KNHANES), conducted from 2009 to 2010. Standardized slit-lamp examinations were performed by study ophthalmologists to examine the anterior segment for evidence of pterygium. Pterygium was graded clinically as T1 (atrophic), T2 (intermediate), or T3 (opaque). Every participant underwent ocular and systemic examinations, as well as interviewer-administered questionnaires. Any evidence of pterygium and observed association between the risk factors were recorded. RESULTS The mean age of the subjects was 55.7 (±0.2) years. Of the 9,193 eligible subjects, 935 had pterygium in at least one eye. In a multivariate logistic regression analysis adjusted for age and sex, pterygium was significantly associated with rural vs. urban residence (odds ratio [OR], 1.7; 95% confidence interval [CI], 1.4 to 2.0), lower level of education (OR, 4.5; 95% CI, 3.1 to 6.6), low income (OR, 1.3; 95% CI, 1.0 to 1.8), smoking (OR, 0.7; 95% CI, 0.5 to 1.0), and more hours of sun exposure (OR, 1.5; 95% CI, 1.2 to 1.8). After adjusting for all variables, the prevalence of pterygium was significantly associated with age, sex, residence, education level, and smoking. CONCLUSIONS This is a nationwide epidemiologic study in South Korea to assess the prevalence of and risk factors for pterygium. The overall prevalence of pterygium was 8.8% among Koreans aged 40 years or older. Older age, male gender, rural residence, lower level of education, and non-smoking were associated with the development of pterygium. PMID:27156345

  3. Epidemiology of venous thromboembolism.

    PubMed Central

    Coon, W W

    1977-01-01

    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

  4. [Acute coronary syndromes: epidemiology].

    PubMed

    Ozkan, Alev Arat

    2013-04-01

    Coronary heart disease is the main cause of death in the world as well as in Turkey. It's not only a health issue but also a social problem with a high economic burden and negative impact on quality of life. The majority of deaths are attributable to acute coronary syndromes (ACS) and their complications.This review summarizes some important facts regarding ACS epidemiology in the world and in Turkey. PMID:27323430

  5. Epidemiology of epilepsy.

    PubMed

    Abramovici, S; Bagić, A

    2016-01-01

    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. PMID:27637958

  6. Future perspectives, applications and challenges of genomic epidemiology studies for food-borne pathogens: A case study of Enterohemorrhagic Escherichia coli (EHEC) of the O157:H7 serotype

    PubMed Central

    Eppinger, Mark; Cebula, Thomas A

    2015-01-01

    The shiga-toxin (Stx)-producing human pathogen Escherichia coli serotype O157:H7 is a highly pathogenic subgroup of Stx-producing E. coli (STEC) with food-borne etiology and bovine reservoir. Each year in the U. S., approximately 100,000 patients are infected with enterohemorrhagic E. coli (EHEC) of the O157:H7 serotype. This food-borne pathogen is a global public health threat responsible for widespread outbreaks of human disease. Since its initial discovery in 1982, O157:H7 has rapidly become the dominant EHEC serotype in North America. Hospitalization rates among patients as high as 50% have been reported for severe outbreaks of human disease. Symptoms of disease can rapidly deteriorate and progress to life-threatening complications such as Hemolytic Uremic Syndrome (HUS), the leading cause of kidney failure in children, or Hemorrhagic Colitis. In depth understanding of the genomic diversity that exists among currently circulating EHEC populations has broad applications for improved molecular-guided biosurveillance, outbreak preparedness, diagnostic risk assessment, and development of alternative toxin-suppressing therapeutics. PMID:25483335

  7. The role of epigenetics in genetic and environmental epidemiology.

    PubMed

    Ladd-Acosta, Christine; Fallin, M Daniele

    2016-02-01

    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.

  8. Complete Genomic Sequence of Duck Flavivirus from China

    PubMed Central

    Liu, Ming; Liu, Chunguo; Li, Gang; Li, Xiaojun; Yin, Xiuchen; Chen, Yuhuan

    2012-01-01

    We report here the complete genomic sequence of the Chinese duck flavivirus TA strain. This work is the first to document the complete genomic sequence of this previously unknown duck flavivirus strain. The sequence will help further relevant epidemiological studies and extend our general knowledge of flaviviruses. PMID:22354941

  9. Whole-genome sequence of Clostridium lituseburense L74, isolated from the larval gut of the rhinoceros beetle, Trypoxylus dichotomus.

    PubMed

    Lee, Yookyung; Lim, Sooyeon; Rhee, Moon-Soo; Chang, Dong-Ho; Kim, Byoung-Chan

    2016-03-01

    Clostridium lituseburense L74 was isolated from the larval gut of the rhinoceros beetle, Trypoxylus dichotomus collected in Yeong-dong, Chuncheongbuk-do, South Korea and subjected to whole genome sequencing on HiSeq platform and annotated on RAST. The nucleotide sequence of this genome was deposited into DDBJ/EMBL/GenBank under the accession NZ_LITJ00000000.

  10. Occurrence of anisakid nematode larvae in chub mackerel (Scomber japonicus) caught off Korea.

    PubMed

    Bak, Tae-Jong; Jeon, Chan-Hyeok; Kim, Jeong-Ho

    2014-11-17

    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. PMID:25268324

  11. Trichinosis: Epidemiology in Thailand

    PubMed Central

    Kaewpitoon, Natthawut; Kaewpitoon, Soraya Jatesadapattaya; Philasri, Chutikan; Leksomboon, Ratana; Maneenin, Chanvit; Sirilaph, Samaporn; Pengsaa, Prasit

    2006-01-01

    Trichinosis is one of the most common food-borne parasitic zoonoses in Thailand and many outbreaks are reported each year. This paper reviews the history, species, and epidemiology of the disease and food habits of the people with an emphasis on the north, northeast, central and south regions of Thailand. The earliest record of trichinosis in Thailand was in 1962 in the Mae Sariang District, Mae Hong Son Province. Since then, about 130 outbreaks have been reported involving 7392 patients and 97 deaths (1962-2005). The highest number of cases, 557, was recorded in 1983. The annual epidemiological surveillance reports of the Bureau of Epidemiology, Department of Disease Control, Ministry of Public Health, Thailand, show that trichinosis cases increased from 61 in 1997 to 351 in 1998. In contrast to these figures, the number of reported cases decreased to 16 in 1999 and 128 cases in 2000. There was no record of trichinosis in 2001, but then the figures for 2002, 2003 and 2004 were 289, 126 and 212 respectively. The infected patients were mostly in the 35-44 years age group and the disease occurred more frequently in men than women at a ratio of 1.7-2.0:1. There were 84 reported cases of trichinosis in Chiang Rai, Nan, Chiang Mai, Si Sa ket, Nakhon Phanom, Kalasin, Nakhon Ratchasima, Nakhon Nayok, Nakhon Pathom and Surat Thani, provinces located in different parts of Thailand in 2005. The outbreaks were more common in the northern areas, especially in rural areas where people ate raw or under-cooked pork and/or wild animals. This indicates the need for health education programs to prevent and control trichinosis as soon as possible in the high-risk areas. PMID:17072975

  12. Epidemiologic research in Antarctica

    NASA Technical Reports Server (NTRS)

    1990-01-01

    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.

  13. Migraine headache: epidemiologic perspectives.

    PubMed

    Linet, M S; Stewart, W F

    1984-01-01

    Clinical and epidemiologic studies suggest that a number of factors are associated with the risk of migraine and precipitation of an attack. However, the degree to which causal associations can be inferred from reported studies is very limited and is a result of the methodological problems discussed throughout this review. The study of migraine in many ways parallels the pattern seen in early investigations of other conditions, such as rheumatoid arthritis and systemic lupus erythematosus, because a number of methodological problems had to be resolved in the study of these conditions before significant progress could be made. To achieve significant advances in the improvement of our understanding of the causes of migraine, a number of related issues must be addressed and resolved in future studies. Most noteworthy among these are Recognition of the probable heterogeneity of migraine, not merely in the manifestation of symptoms but, more importantly, in the existence of distinct etiologic subtypes. A number of findings suggest that some migraine subtypes are sensitive to certain precipitants, some appear to be a part of a more generalized constitutional disorder, and some are accompanied by a higher prevalence of migraine among family members. Efforts should be made in understanding the relationship between specific biochemical markers and traits (such as monoamine oxidase deficiency and tyramine sensitivity); precipitants related to the migraine attack; and epidemiologic characteristics such as age at onset and sex. Creation of a more precise, reliable, and practically useful definition of migraine. Without such a definition, it is difficult, if not impossible, to compare results between studies, to understand the relationship between risk factors and migraine subtypes, to understand properly associations identified in selected clinic populations, and, in general, to understand the epidemiology of migraine. More accurate characterization of the case group under

  14. Prophylaxis of human hydrophobia in South Korea.

    PubMed

    Kim, Yang Ree

    2014-09-01

    Domestic human hydrophobia has not been reported since the one case of 2004 in South Korea, but still a few animal rabies occur persistently since the reemerging stage of rabies from 1993. The government has made efforts to control animal rabies in many aspects, but whether prophylactic strategy for human hydrophobia is performed adequately is in question. The rate of proper post-exposure prophylaxis for animal bite case in 'high-risk region' of rabies is very low with 20% between 2011 and 2013. The National Animal Bite Patient Surveillance targeting 'high-risk region' is missing out animal bite cases who visit directly to hospitals in 'suspect-risk region' of rabies. Little data seems to exist for pre-exposure prophylaxis of domestic hydrophobia. Danger of reoccurrence of human hydrophobia always remain in South Korea. The medical personnel needs to have greater interest on the matter and the government strengthen the management system.

  15. [Epidemiology and control of injury].

    PubMed

    Kim, Soonduck

    2005-05-01

    Injury has recently become a major world-wide health problem. Injury related deaths occur in many actively working young people and produce major social and economical losses. However health related specialists do not recognize the importance of injury and there have not been many studies related to this problem. This research studied the trends of injury related research in Korea, mortality rate and prevalence rate, socio-economical losses and control in Korea and out of the country, based on literature from Korea and without such as statistical yearly reports on causes of deaths and OECD health reports, as well as WHO web sites. Studies in Korea about injury were very few, with 9 in the 1960's, 5 in the 1980's, 4 in the 1990's and 5 in 2000's. Mortality rate of injury was higher in Korea than in England, USA or Japan, especially in car accidents, suicide and falls. In Korea, the yearly trends in mortality rates were highest in car accidents but those rates are falling, suicide is steadily rising, with highest rate in 2003. Falls is in second rank with no change in rates. In 2003, the ten causes of death in Korea were suicide in 5th rank, transport accidents in 7th rank, and falls in 10th rank. Considering age groups, in the teens, transport accidents were 1st rank, in the 20's and 30's, suicide was 1st rank, and although there were some differences, falls, drowning, assault, fire were in the top 10. Prevalence rates of injury could not be known, but in 2001, according to the National Health and Nutrition Survey, lifelong injury was 10%, and yearly major injury was 1.3%, major injury for two weeks was 0.1%, and minor injury was 10%. In other foreign countries, injury has become to be recognized as a major health related problem, and much programs are being set up to reduce injury related deaths and injuries. WHO is putting much effort in prevention of violence and transport accidents, and in the USA, Canada and Europe, there are injury surveillance systems

  16. Is there epidemiology in Russia?

    PubMed Central

    Vlassov, V.

    2000-01-01

    OBJECTIVE—To examine the current state of epidemiology in Russia.
DESIGN—The structure of clinical research and statistical methods was used to shed light on the epidemiology in Russia. The frequencies of specific study designs were evaluated using Medline data for 1970-1997. To determine the proportion of advanced design clinical studies the frequency of cohort, prospective, follow up, or longitudinal studies, and controlled trials was evaluated. All diagnosis related studies were found to determine the usage of advanced statistical technique (ROC analysis). The adequacy of Medline information was checked by hand search of journals. All dissertations in epidemiology defended in Russia in 1995 and 1996 were evaluated for their methodology. The curriculum recommended by Ministry of Health to Medical Universities was evaluated. Available literature and library indexing of epidemiological terms examined.
MAIN RESULTS—Russian medical research uses less frequently advanced study designs and methods of data analysis. Medical students are taught epidemiology as a science of spread of infectious diseases. There is no department of epidemiology in Russian universities where epidemiology is taught in the modern sense and no epidemiological and biostatistical periodicals available in Russia.
CONCLUSION—Epidemiology in Russia remains in an archaic state of science of the spread of infectious diseases and it is detrimental to methodology of medical research in Russia.


Keywords: Soviet Union; Russia; study design; comparative studies PMID:10990475

  17. The People's Library of Epidemiology.

    PubMed

    Last, John M

    2012-03-01

    The People's Library of Epidemiology is in the process of development. It consists of a website (http://www.jameslindlibrary.org) with links to online excerpts of papers and monographs of historical and scientific importance in epidemiology and related public health sciences that are held by the library of the Royal College of Physicians of Edinburgh. This paper reflects the lively panel discussion which took place on 9 August 2011. The panel members who opened the discussion were Alfredo Morabia, Anne Hardy, Roger Bernier, Jan Vandenbroucke, George Davey Smith, Esther Villalonga and Stephen Walter, who had won the prize awarded by Epidemiology Monitor for an essay on the People's Library of Epidemiology.

  18. Achievements in and Challenges of Tuberculosis Control in South Korea.

    PubMed

    Kim, Ji Han; Yim, Jae-Joon

    2015-11-01

    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.

  19. Tritium production, recovery and application in Korea.

    PubMed

    Son, Soon-Hwan; Lee, Sook-Kyung; Kim, Kwang-Sin

    2009-01-01

    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. PMID:19307127

  20. Green Chemistry at the present in Korea

    PubMed Central

    Lee, Seung-Kyu; Park, Hyeon-Soo

    2015-01-01

    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

  1. Metalimnobia crane flies (Diptera: Limoniidae) from Korea.

    PubMed

    Podenas, Sigitas; Byun, Hye-Woo

    2016-01-01

    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. PMID:27395675

  2. Mortality from and incidence of pesticide poisoning in South Korea: findings from National Death and Health Utilization Data between 2006 and 2010.

    PubMed

    Cha, Eun Shil; Khang, Young-Ho; Lee, Won Jin

    2014-01-01

    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.

  3. Epidemiological evidences on overdiagnosis of prostate and kidney cancers in Korean

    PubMed Central

    Bae, Jong-Myon

    2015-01-01

    OBJECTIVES: The prostate specific antigen test is widely used as the main method of screening prostate cancer in Korea. Additionally, the use of ultrasound sonography may lead to overdiagnosis of kidney cancer as well as thyroid cancer. This study aimed to highlight epidemiological evidences regarding overdiagnosis of prostate and kidney cancers in Korean. METHODS: The annual trends of national incidence and mortality of prostate and kidney cancers provided by the Korean Statistical Information Service were evaluated. RESULTS: The rate of increase in the incidence of prostate and kidney cancer was 6 and 5 times higher than that of mortality between 2000 and 2011, respectively. Additionally, the age group showing the highest incidence in prostate cancer shifted from 85 years and older to 75-79 years. CONCLUSIONS: This evidence suggests that prostate and kidney cancers are overdiagnosed in Korea. Further research in this area, using national cancer registry databases, should be encouraged to prevent overdiagnosis. PMID:25773442

  4. Proving Causation With Epidemiological Evidence in Tobacco Lawsuits

    PubMed Central

    2016-01-01

    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

  5. Epidemiology of rickettsial diseases.

    PubMed

    Walker, D H; Fishbein, D B

    1991-05-01

    Rickettsial diseases have a diversity of epidemiologic characteristics reflective of the variety of ecologic situations in which the obligate intracellular bacteria are transmitted to humans. For the spotted fever group (SFG) rickettsiae, Rickettsia typhi, R. tsutsugamushi, Coxiella burnetii, and the human ehrlichial agent, humans are a dead-end host who plays no role in the maintenance of the organism in nature. All rickettsioses exist as zoonoses. Moreover, all rickettsiae are found in infected arthopods, which generally serve as the natural hosts and can transmit the infection to the next generation of ticks, mites, chiggers, or fleas. From our anthropocentric viewpoint, Q fever aerosol infection from parturient animals and Brill-Zinsser disease ignited epidemics of louse-borne epidemic typhus are exceptions. However, silent cycles of C. burnetii in ticks and R. prowazekii in the flying squirrel flea may have maintained these agents in transovarial or enzootic cycles for eons before humans and their domestic animals arrived on the scene. Thus, the epidemiology of rickettsial diseases must be recognized as an unfortunate aberration of the rickettsial economy. Several excellent reviews of rickettsial ecology contain a wealth of useful information. PMID:1884775

  6. The Epidemiology of Sarcopenia.

    PubMed

    Dodds, Richard Matthew; Roberts, Helen Clare; Cooper, Cyrus; Sayer, Avan Aihie

    2015-01-01

    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.

  7. Epidemiology, austerity, and innovation.

    PubMed

    Samet, Jonathan M; Ness, Roberta B

    2012-05-15

    In considering the state of epidemiologic research, these are the "best" and the "worst" of times-the "best" from the perspective of scientific opportunities and the "worst" from the perspective of funding. In this commentary, the authors address this time of funding austerity from the points of view of individual researchers and research institutions. For researchers, the new tools of "-omics," large databases, communication by means of the World Wide Web, and global access offer ever-expanding scientific opportunities. The authors comment on research directions for which there is an enhanced likelihood of funding success: clinical and translational research, outcomes and effectiveness research, and global health research. The authors emphasize the need to be innovative and not bound by the conventional. For institutions, the authors suggest attention to innovation and impact, social networking, and finding the "right size" for training programs. Academic institutions also need to invest, supporting researchers and their ideas. Epidemiologists need to be true to their mission and prove that they can use innovation to advance health and welfare in a measurable way. Doing so will ensure that over the long term, epidemiologic research will remain a cornerstone for advancing population health.

  8. Ecogeographic Genetic Epidemiology

    PubMed Central

    Sloan, Chantel D.; Duell, Eric J.; Shi, Xun; Irwin, Rebecca; Andrew, Angeline S.; Williams, Scott M.; Moore, Jason H.

    2009-01-01

    Complex diseases such as cancer and heart disease result from interactions between an individual's genetics and environment, i.e. their human ecology. Rates of complex diseases have consistently demonstrated geographic patterns of incidence, or spatial “clusters” of increased incidence relative to the general population. Likewise, genetic subpopulations and environmental influences are not evenly distributed across space. Merging appropriate methods from genetic epidemiology, ecology and geography will provide a more complete understanding of the spatial interactions between genetics and environment that result in spatial patterning of disease rates. Geographic Information Systems (GIS), which are tools designed specifically for dealing with geographic data and performing spatial analyses to determine their relationship, are key to this kind of data integration. Here the authors introduce a new interdisciplinary paradigm, ecogeographic genetic epidemiology, which uses GIS and spatial statistical analyses to layer genetic subpopulation and environmental data with disease rates and thereby discern the complex gene-environment interactions which result in spatial patterns of incidence. PMID:19025788

  9. Global epidemiology of sporotrichosis.

    PubMed

    Chakrabarti, Arunaloke; Bonifaz, Alexandro; Gutierrez-Galhardo, Maria Clara; Mochizuki, Takashi; Li, Shanshan

    2015-01-01

    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.

  10. Epidemiology of bronchioloalveolar carcinoma.

    PubMed

    Falk, R T; Pickle, L W; Fontham, E T; Greenberg, S D; Jacobs, H L; Correa, P; Fraumeni, J F

    1992-01-01

    Descriptive features of bronchioloalveolar carcinoma (BAC) are presented using Surveillance, Epidemiology and End Results Program population-based incidence data from 1973 through 1987, along with risk factors from histologically confirmed cases of BAC identified in a hospital-based case-control study conducted in Louisiana between 1979 and 1982. Compared to the rising incidence of lung cancer overall, BAC rates have remained relatively constant, accounting for less than 3% of all lung cancer. BAC incidence rates were higher in males, yet it explained proportionately more of the total lung cancer incidence in females. In the case-control study, 21 of the 33 cases originally ascertained from hospital pathology records were histologically confirmed as BAC. Most cases smoked cigarettes, with a 4-fold risk for ever smoking. Risks tended to increase with smoking intensity (reaching 10-fold for more than 1.5 packs/day) and duration (reaching 5-fold for more than 45 years of smoking). Following 10 or more years of employment, there was a 4-fold risk associated with motor freight occupations, along with nonsignificant excesses among construction workers, petroleum manufacturers, and sugar cane farmers. Cases were more likely than controls to have had emphysema or to have had a close family member with lung cancer. Although based on small numbers, this study suggests that BAC shares many of the epidemiological characteristics of lung adenocarcinoma.

  11. Epidemiology of Neuroendocrine Tumors.

    PubMed

    Fraenkel, Merav; Faggiano, Antongiulio; Valk, Gerlof D

    2015-01-01

    Formerly named carcinoids, neuroendocrine tumors originate from diffuse endocrine cells, can involve any part of the gastrointestinal tract, endocrine pancreas and bronchopulmonary (BP) tree, and have a wide range of malignant potential. This chapter summarizes the data available on the epidemiology of neuroendocrine neoplasia (NEN) from around the world, including the relative frequency according to organ of origin, annual incidence rates (IR) and trends in IR at the various anatomic sites, age and stage at presentation, racial and gender differences in IR and 5-year survival rates. Over time, changes have been made in the classification and registration of NEN, both in the same registry and across the globe, thus confounding the possibility to draw conclusions as to the true rise in IR of NEN that is observed all over the world. BP NEN has become the most common site in many western countries, while NEN of the rectum is more common in the Far East. In some countries, appendiceal NEN is the most common site in females. When compared to adenocarcinoma of the same location, the prognosis of NEN patients is better. Five-year survival rates are highest for NEN originating in the rectum and appendix, but lower in small intestinal and pancreatic NEN. Future research is needed to understand the contribution of genetic and environmental factors to NEN epidemiology. PMID:26303701

  12. 77 FR 33181 - Large Residential Washers From the Republic of Korea: Preliminary Affirmative Countervailing Duty...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-06-05

    ... Washers From the Republic of Korea: Initiation of Countervailing Duty Investigation, 77 FR 4279 (January... Korea: Postponement of Preliminary Determination in the Countervailing Duty Investigation, 77 FR 13559... Korea: Final Affirmative Countervailing Duty Determination, 77 FR 17410 (March 26, 2012)...

  13. Complete genome of Kangiella geojedonensis KCTC 23420(T), putative evidence for recent genome reduction in marine environments.

    PubMed

    Choe, Hanna; Kim, Seil; Oh, Jeongsu; Nasir, Arshan; Kim, Byung Kwon; Kim, Kyung Mo

    2015-12-01

    Kangiella geojedonensis KCTC 23420(T) is an aerobic, Gram-negative, non-motile, non-spore-forming, rod-shaped bacterium that was isolated from seawater off the southern coast of Korea. We here report the complete genome of K. geojedonensis KCTC 23420(T), which consists of 2,495,242 bp (G+C content of 43.78%) with 2,257 protein-coding genes, 41 tRNAs, 2 rRNA operons. The genome is smaller than the other closely related genomes, indicating that K. geojedonensis has recently experienced reductive evolution.

  14. Complete genome of Kangiella geojedonensis KCTC 23420(T), putative evidence for recent genome reduction in marine environments.

    PubMed

    Choe, Hanna; Kim, Seil; Oh, Jeongsu; Nasir, Arshan; Kim, Byung Kwon; Kim, Kyung Mo

    2015-12-01

    Kangiella geojedonensis KCTC 23420(T) is an aerobic, Gram-negative, non-motile, non-spore-forming, rod-shaped bacterium that was isolated from seawater off the southern coast of Korea. We here report the complete genome of K. geojedonensis KCTC 23420(T), which consists of 2,495,242 bp (G+C content of 43.78%) with 2,257 protein-coding genes, 41 tRNAs, 2 rRNA operons. The genome is smaller than the other closely related genomes, indicating that K. geojedonensis has recently experienced reductive evolution. PMID:26044616

  15. Genomic Motifs as a Novel Indicator of the Relationship between Strains Isolated from the Epidemic of Porcine Epidemic Diarrhea in 2013-2014.

    PubMed

    Yamamoto, Takehisa; Suzuki, Tohru; Ohashi, Seiichi; Miyazaki, Ayako; Tsutsui, Toshiyuki

    2016-01-01

    Porcine epidemic diarrhea virus (PEDV) is a positive-sense RNA virus that causes infectious gastroenteritis in pigs. Following a PED outbreak that occurred in China in 2010, the disease was identified for the first time in the United States in April 2013, and was reported in many other countries worldwide from 2013 to 2014. As a novel approach to elucidate the epidemiological relationship between PEDV strains, we explored their genome sequences to identify the motifs that were shared within related strains. Of PED outbreaks reported in many countries during 2013-2014, 119 PEDV strains in Japan, USA, Canada, Mexico, Germany, and Korea were selected and used in this study. We developed a motif mining program, which aimed to identify a specific region of the genome that was exclusively shared by a group of PEDV strains. Eight motifs were identified (M1-M8) and they were observed in 41, 9, 18, 6, 10, 14, 2, and 2 strains, respectively. Motifs M1-M6 were shared by strains from more than two countries, and seemed to originate from one PEDV strain, Indiana12.83/USA/2013, among the 119 strains studied. BLAST search for motifs M1-M6 revealed that M3-M5 were almost identical to the strain ZMDZY identified in 2011 in China, while M1 and M2 were similar to other Chinese strains isolated in 2011-2012. Consequently, the PED outbreaks in these six countries may be closely related, and multiple transmissions of PEDV strains between these countries may have occurred during 2013-2014. Although tools such as phylogenetic tree analysis with whole genome sequences are increasingly applied to reveal the connection between isolates, its interpretation is sometimes inconclusive. Application of motifs as a tool to examine the whole genome sequences of causative agents will be more objective and will be an explicit indicator of their relationship. PMID:26808527

  16. Planning for the Future of Epidemiology in the Era of Big Data and Precision Medicine

    PubMed Central

    Khoury, Muin J.

    2015-01-01

    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. PMID:26628513

  17. Planning for the Future of Epidemiology in the Era of Big Data and Precision Medicine.

    PubMed

    Khoury, Muin J

    2015-12-15

    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.

  18. An Epidemiological Study of Hyperhidrosis Patients Visiting the Ajou University Hospital Hyperhidrosis Center in Korea

    PubMed Central

    Park, Eun Jung; Han, Kyung Ream; Choi, Ho; Kim, Do Wan

    2010-01-01

    Hyperhidrosis is a disorder of perspiration in excess of the body's physiologic need and significantly impacts one's occupational, physical, emotional, and social life. The purpose of our study was to investigate the characteristics of primary hyperhidrosis in 255 patients at Ajou University Hospital Hyperhidrosis Center from March 2006, to February 2008. Information collected from the medical records was: sex, sites of hyperhidrosis, age at visit, age of onset, aggravating factors, hyperhidrosis disease severity scale (HDSS) rank, family history, occupation, and past treatment. A total of 255 patient records were reviewed; 57.6% were male. Patients with a family history (34.1%) showed a lower age of onset (13.21±5.80 yr vs. 16.04±9.83 yr in those without family history); 16.5% had previous treatment, most commonly oriental medicine. Palmar and plantar sites were the most commonly affected, and 87.9% of patients felt their sweating was intolerable and always interfered with their daily activities. Our study provides some original information on the Korean primary hyperhidrosis population. Patients who have a family history show signs of disease in early age than those without family history. PMID:20436716

  19. Concordance and discordance of sequence survey methods for molecular epidemiology

    PubMed Central

    Hasan, Nur A.; Cebula, Thomas A.; Colwell, Rita R.; Robison, Richard A.; Johnson, W. Evan; Crandall, Keith A.

    2015-01-01

    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

  20. Molecular genetic analysis of cucumber mosaic virus populations infecting pepper suggests unique patterns of evolution in Korea.

    PubMed

    Kim, Mi-Kyeong; Seo, Jang-Kyun; Kwak, Hae-Ryun; Kim, Jeong-Soo; Kim, Kook-Hyung; Cha, Byeong-Jin; Choi, Hong-Soo

    2014-09-01

    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.

  1. Molecular analyses of H3N2 canine influenza viruses isolated from Korea during 2013-2014.

    PubMed

    Lee, EunJung; Kim, Eun-Ju; Kim, Bo-Hye; Song, Jae-Young; Cho, In-Soo; Shin, Yeun-Kyung

    2016-04-01

    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.

  2. Molecular genetic analysis of cucumber mosaic virus populations infecting pepper suggests unique patterns of evolution in Korea.

    PubMed

    Kim, Mi-Kyeong; Seo, Jang-Kyun; Kwak, Hae-Ryun; Kim, Jeong-Soo; Kim, Kook-Hyung; Cha, Byeong-Jin; Choi, Hong-Soo

    2014-09-01

    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. PMID:25116642

  3. Risk Factors and Control Strategies for the Rapidly Rising Rate of Breast Cancer in Korea

    PubMed Central

    Park, Sue K.; Kim, Yeonju; Kang, Daehee; Jung, En-Joo

    2011-01-01

    Due to the aging population and tremendous changes in life style over the past decades, cancer has been the leading cause of death in Korea. The incidence rate of breast cancer is the second highest in Korea, and it has shown an annual increase of 6.8% for the past 6 years. The major risk factors of breast cancer in Korean women are as follows: Early menarche, late menopause, late full-term pregnancy (FTP), and low numbers of FTP. Height and body mass index increased the risk of breast cancer in postmenopausal women only. There are ethnic variations in breast cancer due to the differences in genetic susceptibility or exposure to etiologic agent. With the epidemiological evidences on the possibility of further increase of breast cancer in Korea, the Korean Government began implementing the National Cancer Screening Program against breast cancer in 2002. Five-year survival rates for female breast cancer have improved significantly from 78.0% in early 1993-1995 to 90.0% in 2004-2008. This data indicate that improvement of the survival rate may be partially due to the early diagnosis of breast cancer as well as the increased public awareness about the significance of early detection and organized cancer screening program. The current primary prevention programs are geared towards strengthening national prevention campaigns. In accordance with the improvement in 5-year survival rate, the overall cancer mortality has started to decrease. However, breast cancer death rate and incidence rates are still increasing, which need further organized effort by the Korean Government. PMID:21847401

  4. Prevalence and Molecular Characteristics of Carbapenemase-Producing Enterobacteriaceae From Five Hospitals in Korea

    PubMed Central

    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

    2016-01-01

    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

  5. The new epidemiology of nephrolithiasis.

    PubMed

    Shoag, Jonathan; Tasian, Greg E; Goldfarb, David S; Eisner, Brian H

    2015-07-01

    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. PMID:26088071

  6. Ethical issues in epidemiological research.

    PubMed

    Hessel, P A; Fourie, P B

    1987-12-19

    Ethical concerns pervade all aspects of epidemiological investigations. Ethical issues, including planning, carrying out, analysing and presenting the results of a study, are discussed. In southern Africa, where many community-based epidemiological surveys are undertaken, issues relating specifically to the conduct of such studies are especially relevant. These include informed consent, confidentiality and privacy.

  7. CEDR: Comprehensive Epidemiologic Data Resource

    SciTech Connect

    Not Available

    1993-08-01

    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.

  8. The First Case of Capillaria hepatica Infection in a Nutria (Myocastor coypus) in Korea

    PubMed Central

    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

    2014-01-01

    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

  9. Epidemiological evidence in forensic pharmacovigilance.

    PubMed

    Persaud, Nav; Healy, David

    2012-01-01

    Until recently epidemiological evidence was not regarded as helpful in determining cause and effect. It generated associations that then had to be explained in terms of bio-mechanisms and applied to individual patients. A series of legal cases surrounding possible birth defects triggered by doxylamine (Bendectin) and connective tissue disorders linked to breast implants made it clear that in some instances epidemiological evidence might have a more important role, but the pendulum swung too far so that epidemiological evidence has in recent decades been given an unwarranted primacy, partly perhaps because it suits the interests of certain stakeholders. Older and more recent epidemiological studies on doxylamine and other antihistamines are reviewed to bring out the ambiguities and pitfalls of an undue reliance on epidemiological studies.

  10. Clustering of Mycobacterium tuberculosis strains from foreign-born patients in Korea.

    PubMed

    Jeon, Christie Y; Kang, Heeyoon; Kim, Mihye; Murray, Megan B; Kim, Heejin; Cho, Eun Hee; Park, Young Kil

    2011-12-01

    Information on drug resistance and transmission patterns of tuberculosis (TB) in foreign-born patients is lacking in Asia where immigration is increasing. We examined the drug-resistance profiles of 288 Mycobacterium tuberculosis isolates from foreign-born patients in South Korea, and assessed for potential transmission in the host country by analysing their IS6110 genotypes, as well as those of 4780 strains from native Korean TB patients. The prevalence of multidrug-resistant (MDR) TB was 9.7% and 42% among new and previously treated patients, respectively. Chinese nationality was associated with MDR TB (OR(China)=3.0, 95% CI 1.1-9.3). Of the 288 strains, 51 (17.7%) formed 31 clusters, of which 22 were identical to strains from native Koreans. A number of strains belonged to the K family, subtypes known to occur endemically in Korea. MDR TB was common, and clustering patterns showed potential cross-cultural transmission among foreign-born TB patients. Further molecular epidemiological studies of all isolates in the area are needed to determine the extent of international TB transmission in Asia.

  11. Prevalence of Trichomonas vaginalis in Women Visiting 2 Obstetrics and Gynecology Clinics in Daegu, South Korea.

    PubMed

    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

    2016-02-01

    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. PMID:26951983

  12. DISTRIBUTION OF LEGIONELLA PNEUMOPHILA SEROGROUPS ISOLATED FROM WATER SYSTEMS OF PUBLIC FACILITIES IN BUSAN, SOUTH KOREA.

    PubMed

    Hwang, In-Yeong; Park, Eun-Hee; Park, Yon-Koung; Park, Sun-Hee; Sung, Gyung-Hye; Park, Hye-Young; Lee, Young-Choon

    2016-05-01

    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. PMID:27405130

  13. Prevalence of Trichomonas vaginalis in Women Visiting 2 Obstetrics and Gynecology Clinics in Daegu, South Korea

    PubMed Central

    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

    2016-01-01

    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. PMID:26951983

  14. Prevalence of treated epilepsy in Korea based on national health insurance data.

    PubMed

    Lee, Seo-Young; Jung, Ki-Young; Lee, Il Keun; Yi, Sang Do; Cho, Yong Won; Kim, Dong Wook; Hwang, Seung-Sik; Kim, Sejin

    2012-03-01

    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.

  15. Applying molecular epidemiology in pediatric leukemia.

    PubMed

    Schiffman, Joshua D

    2016-02-01

    Molecular epidemiology is the study of genetic and environmental risk for disease, with much effort centered on cancer. Childhood leukemia occurs in nearly a third of all patients newly diagnosed with pediatric cancer. only a small percentage of these new cases of childhood leukemia are associated with high penetrant hereditary cancer syndromes. Childhood leukemia, especially acute lymphoblastic leukemia, has been associated with a dysregulated immune system due to delayed infectious exposure at a young age. Identical twins with childhood leukemia suggest that acute lymphoblastic leukemia begins in utero and that the concordant presentation is due to a shared preleukemia subclone via placental transfer. Investigation of single nucleotide polymorphisms within candidate genes find that leukemia risk may be attributed to population-based polymorphisms affecting folate metabolism, xenobiotic metabolism, DNA repair, immunity, and B-cell development. More recently, genome-wide association studies for leukemia risk has led investigators to genes associated with B-cell development. When describing leukemia predisposition due to hereditary cancer syndromes, the following 6 categories become apparent on the basis of biology and clinical presentation: (1) genetic instability/DNA repair syndromes, (2) cell cycle/differentiation syndromes, (3) bone marrow failure syndromes, (4) telomere maintenance syndromes, (5) immunodeficiency syndromes, and (6) transcription factor syndromes and pure familial leukemia. understanding the molecular epidemiology of childhood leukemia can affect the treatment and tumor surveillance strategies for these high risk patients and their family members.

  16. Applying molecular epidemiology in pediatric leukemia.

    PubMed

    Schiffman, Joshua D

    2016-02-01

    Molecular epidemiology is the study of genetic and environmental risk for disease, with much effort centered on cancer. Childhood leukemia occurs in nearly a third of all patients newly diagnosed with pediatric cancer. only a small percentage of these new cases of childhood leukemia are associated with high penetrant hereditary cancer syndromes. Childhood leukemia, especially acute lymphoblastic leukemia, has been associated with a dysregulated immune system due to delayed infectious exposure at a young age. Identical twins with childhood leukemia suggest that acute lymphoblastic leukemia begins in utero and that the concordant presentation is due to a shared preleukemia subclone via placental transfer. Investigation of single nucleotide polymorphisms within candidate genes find that leukemia risk may be attributed to population-based polymorphisms affecting folate metabolism, xenobiotic metabolism, DNA repair, immunity, and B-cell development. More recently, genome-wide association studies for leukemia risk has led investigators to genes associated with B-cell development. When describing leukemia predisposition due to hereditary cancer syndromes, the following 6 categories become apparent on the basis of biology and clinical presentation: (1) genetic instability/DNA repair syndromes, (2) cell cycle/differentiation syndromes, (3) bone marrow failure syndromes, (4) telomere maintenance syndromes, (5) immunodeficiency syndromes, and (6) transcription factor syndromes and pure familial leukemia. understanding the molecular epidemiology of childhood leukemia can affect the treatment and tumor surveillance strategies for these high risk patients and their family members. PMID:25973690

  17. [Epidemiological problems of obesity].

    PubMed

    Beiul, E A; Oleneva, V A; Mühr, M; Heller, G M; Popova, Iu P

    1980-01-01

    The results of epidemiological survey of the population living in the middle zone of the Soviet Union and in the GDR are considered. Comparison of the data obtained shows that overweight is a very prevalent abnormal condition among the test population groups in both countries and amounts to 26% (USSR) and 30% (GDR). Excess animal fat consumption in the presence of a decreased quota of vegetable oil has been established and a significant increase in monosaccharides intake noted. Attention is attracted by insufficient quota of fresh vegetables and fruit in the diets of the population of both countries. Qualitative and quantitative nutritional pitfalls were shown to be aggravated in obese people. Violation of dietetic regimens and decreased physical activity play a definite role in the development of overweight. A program on primary and secondary prevention of overweight has been established. It includes a number of measures both common and specific to the GDR and the USSR.

  18. Melanoma Epidemiology and Prevention.

    PubMed

    Berwick, Marianne; Buller, David B; Cust, Anne; Gallagher, Richard; Lee, Tim K; Meyskens, Frank; Pandey, Shaily; Thomas, Nancy E; Veierød, Marit B; Ward, Sarah

    2016-01-01

    The epidemiology of melanoma is complex, and individual risk depends on sun exposure, host factors, and genetic factors, and in their interactions as well. Sun exposure can be classified as intermittent, chronic, or cumulative (overall) exposure, and each appears to have a different effect on type of melanoma. Other environmental factors, such as chemical exposures-either through occupation, atmosphere, or food-may increase risk for melanoma, and this area warrants further study. Host factors that are well known to be important are the numbers and types of nevi and the skin phenotype. Genetic factors are classified as high-penetrant genes, moderate-risk genes, or low-risk genetic polymorphisms. Subtypes of tumors, such as BRAF-mutated tumors, have different risk factors as well as different therapies. Prevention of melanoma has been attempted using various strategies in specific subpopulations, but to date optimal interventions to reduce incidence have not emerged. PMID:26601858

  19. Cancer epidemiology of woodworking.

    PubMed

    Mohtashamipur, E; Norpoth, K; Lühmann, F

    1989-01-01

    The literature published between 1965 and 1989 on the cancer epidemiology of woodworking in furniture industries and carpentry shops in 17 countries is reviewed. Included are some unpublished data obtained through personal communication with epidemiologists or collected from doctoral dissertations. Of 5,785 cases with sino-nasal cancers, about 23% were found to be woodworkers. Dusty jobs, especially wood processing using high-speed machines, are mainly associated with the enhanced incidence of nasal adenocarcinomas. The latency periods of the latter tumors ranged from 7 to 69 years in five European countries. A variety of neoplasias of the respiratory, digestive, and urinary tracts as well as the hemopoietic and lymphatic systems, including Hodgkin's disease are reported to be significantly associated with occupational exposure to wood dust. These data suggest that the exposure to some types of wood dust might cause a systemic rather than local neoplastic disorder.

  20. EPIDEMIOLOGY OF PARACOCCIDIOIDOMYCOSIS

    PubMed Central

    MARTINEZ, Roberto

    2015-01-01

    SUMMARY The epidemiological characteristics of paracoccidioidomycosis were reviewed and updated. The new endemic areas in Brazil were discussed in the section regarding the geographic distribution of the mycosis. Subclinical infection with Paracoccidioides brasiliensis was discussed on the basis of skin test surveys with antigens of the fungus, seroepidemiological studies, and disease cases outside Latin America. Large case series permitted a comparison of the prevalence of the mycosis in different regions, its estimated incidence and risk factors for the development of the disease. Aspects modulating the expression of the clinical forms of paracoccidioidomycosis are also presented. This review also deals with diseases associated with the mycosis, opportunistic paracoccidioidomycosis, lethality, mortality and infection and disease in animals. PMID:26465364

  1. [Epidemiology of tuberculosis].

    PubMed

    Mjid, M; Cherif, J; Ben Salah, N; Toujani, S; Ouahchi, Y; Zakhama, H; Louzir, B; Mehiri-Ben Rhouma, N; Beji, M

    2015-01-01

    Tuberculosis is a contagious disease caused by Mycobacterium tuberculosis. It represents, according to World Health Organization (WHO), one of the most leading causes of death worldwide. With nearly 8 million new cases each year and more than 1 million deaths per year, tuberculosis is still a public health problem. Despite of the decrease in incidence, morbidity and mortality remain important partially due to co-infection with human immunodeficiency virus and emergence of resistant bacilli. All WHO regions are not uniformly affected by TB. Africa's region has the highest rates of morbidity and mortality. The epidemiological situation is also worrying in Eastern European countries where the proportion of drug-resistant tuberculosis is increasing. These regional disparities emphasize to develop screening, diagnosis and monitoring to the most vulnerable populations. In this context, the Stop TB program, developed by the WHO and its partner's, aims to reduce the burden of disease in accordance with the global targets set for 2015.

  2. Molecular identification of anisakid nematodes third stage larvae isolated from common squid ( Todarodes pacificus) in Korea

    NASA Astrophysics Data System (ADS)

    Setyobudi, Eko; Jeon, Chan-Hyeok; Choi, Kwangho; Lee, Sung Il; Lee, Chung Il; Kim, Jeong-Ho

    2013-06-01

    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.

  3. Epidemiology of HCV infection.

    PubMed

    Baldo, V; Baldovin, T; Trivello, R; Floreani, A

    2008-01-01

    It is estimated that approximately 130-170 million people worldwide are infected with hepatitis C virus (HCV). According to data from WHO community and blood donor surveys, the African and Eastern Mediterranean countries report the highest prevalence rates (>10%). The rates of infection in the general population and the incidence of newly-acquired cases indicate an appreciable change in the epidemiology of the infection in recent years. Prior to the widespread screening of blood donations, infected blood and blood products represented a common source of infection. On the other hand, the high peak in HCV antibodies among the elderly in Italian epidemiological studies on the population at large reflects a cohort effect due to an epidemic of HCV infection occurring after the Second World War. According to data reported by the CDC Surveillance System, the incidence of acute hepatitis C has declined since the late 1980s. In 2005, as in previous years, the majority of such cases in North America and Northern Europe occurred among young adults and injected drug use was the most common risk factor. Other, less commonly reported modes of HCV acquisition are occupational exposure to blood, high-risk sexual activity, tattooing, body piercing and other forms of skin penetration. Finally, the overall rate of mother-to-child transmission from HCV-infected, HIV-negative mothers has been estimated at around 5% (coinfection with HIV raises this figure to 19.4%). HCV prevention relies on identifying and counseling uninfected persons at risk of contracting hepatitis C. PMID:18673187

  4. Epidemiology of acne vulgaris.

    PubMed

    Bhate, K; Williams, H C

    2013-03-01

    Despite acne being an almost universal condition in younger people, relatively little is known about its epidemiology. We sought to review what is known about the distribution and causes of acne by conducting a systematic review of relevant epidemiological studies. We searched Medline and Embase to the end of November 2011. The role of Propionibacterium acnes in pathogenesis is unclear: antibiotics have a direct antimicrobial as well as an anti-inflammatory effect. Moderate-to-severe acne affects around 20% of young people and severity correlates with pubertal maturity. Acne may be presenting at a younger age because of earlier puberty. It is unclear if ethnicity is truly associated with acne. Black individuals are more prone to postinflammatory hyperpigmentation and specific subtypes such as 'pomade acne'. Acne persists into the 20s and 30s in around 64% and 43% of individuals, respectively. The heritability of acne is almost 80% in first-degree relatives. Acne occurs earlier and is more severe in those with a positive family history. Suicidal ideation is more common in those with severe compared with mild acne. In the U.S.A., the cost of acne is over 3 billion dollars per year in terms of treatment and loss of productivity. A systematic review in 2005 found no clear evidence of dietary components increasing acne risk. One small randomized controlled trial showed that low glycaemic index (GI) diets can lower acne severity. A possible association between dairy food intake and acne requires closer scrutiny. Natural sunlight or poor hygiene are not associated. The association between smoking and acne is probably due to confounding. Validated core outcomes in future studies will help in combining future evidence.

  5. Epidemiology of dental caries.

    PubMed

    Winter, G B

    1990-01-01

    The most recent epidemiological data on the prevalence of dental caries in children indicate a halting of the increasing levels in many developing countries and a continuing decrease in many highly industrialized countries of the world. However, a further fall in caries levels predicted for 5-yr-old children in the U.K. has not occurred and the decline in caries may have begun to level out. 'Polarization' of caries to a minority of high-risk individuals is occurring in the developed world, with 20-25% of children accounting for more than 50% of the disease. Socio-economic factors are important in determining the proportion of high-risk children in these countries. The multifactorial aetiology of caries allows a number of different interpretations to account for changes in the prevalence of the disease with time, in both the developing and developed countries. These changes are variously ascribed to alterations in dietary habits, especially the consumption of sugar; variations in the patterns of oral hygiene; increased contact with trace elements, especially fluoride, in the environment; changes in the ecology and/or virulence of oral and dental plaque microflora and alterations in the oral protective mechanisms including the immune status. The epidemiological evidence available on the relationship of all these social, environmental and other factors to changes in the prevalence levels of caries does not, however, fully explain all the changes that have been observed. The claim that caries is no longer a public health problem is premature, as it ignores the still high proportion of individuals with tooth decay throughout the world.

  6. School Expansion in North Korea and South Korea: Two Systems, Two Approaches.

    ERIC Educational Resources Information Center

    Lee, Hyangkue

    2001-01-01

    Examines differences in the public-policy objectives and financing of school expansion efforts in North and South Korea. Institutionalizing credentialism and reliance on financing private education dominates South Korean school expansion, while the financing of public schools and greater government control of education dominates North Korean…

  7. Sexual Violence among Men in the Military in South Korea

    ERIC Educational Resources Information Center

    Kwon, Insook; Lee, Dong-Ok; Kim, Elli; Kim, Hyun-Young

    2007-01-01

    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…

  8. An Ecological Understanding of Youth Suicide in South Korea

    ERIC Educational Resources Information Center

    Lee, Seung-yeon; Hong, Jun Sung; Espelage, Dorothy L.

    2010-01-01

    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…

  9. Integrating Standardization into Engineering Education: The Case of Forerunner Korea

    ERIC Educational Resources Information Center

    Choi, Dong Geun; de Vries, Henk J.

    2013-01-01

    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…

  10. 76 FR 54790 - Large Power Transformers From Korea

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-09-02

    ..., and by publishing the notice in the Federal Register of July 20, 2011 (76 FR 43343). The conference... 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...

  11. 77 FR 52758 - Large Power Transformers From Korea

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-30

    ... publishing the notice in the Federal Register of March 21, 2012 (77 FR 16559). The hearing was held in... 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...

  12. English Education and Teacher Education in South Korea

    ERIC Educational Resources Information Center

    Jo, Seongja

    2008-01-01

    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…

  13. Motivations and Experiences of Expatriate Educators in South Korea

    ERIC Educational Resources Information Center

    Oliver, Nicolette

    2009-01-01

    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…

  14. South Korea: Language Policy and Planning in the Making

    ERIC Educational Resources Information Center

    Song, Jae Jung

    2012-01-01

    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…

  15. 77 FR 51569 - Large Residential Washers From Korea and Mexico

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-24

    ... amendments took effect on November 7, 2011. See 76 FR 61937 (Oct. 6, 2011) and the newly revised Commission's... COMMISSION Large Residential Washers From Korea and Mexico Scheduling of the final phase of countervailing...-fair-value imports from Korea and Mexico of large residential washers, provided for in subheading...

  16. Today and Yesterday in Early Childhood Education in Korea.

    ERIC Educational Resources Information Center

    Lee, Guang-Lea

    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 describes the…

  17. The Beginnings of Modern Education in Korea, 1883-1910

    ERIC Educational Resources Information Center

    Dittrich, Klaus

    2014-01-01

    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…

  18. Globalization and Higher Education: A South Korea Perspective

    ERIC Educational Resources Information Center

    Lee, Jeong-Kyu

    2004-01-01

    The purpose of this paper is to examine globalization and higher education from a perspective of South Korea. First, the paper reviews the concepts of globalization and internationalization. Second, the author describes a historical synopsis regarding internationalization and higher education in South Korea. Third, Korean government policies on…

  19. Three New Records of Lichen Genus Rhizocarpon from South Korea

    PubMed Central

    Joshi, Yogesh; Koh, Young Jin

    2010-01-01

    The paper describes three new records of lichen genus Rhizocarpon (R. alpicola, R. grande and R. lavatum) from South Korea. Brief taxonomic description and comments are provided for the new records. An artificial key is also provided for known species of this genus in South Korea. PMID:23956659

  20. 75 FR 38158 - Korea Finance Corporation; Notice of Application

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-07-01

    ... institution ] established by the government of the Republic of Korea (the ``Korean Government'') requests an...-owned policy finance institution established by the Korean Government on October 28, 2009, pursuant to the Korea Finance Corporation Act (the ``KoFC Act''). The Korean Government established Applicant...