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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. The Association between Parameters of Socioeconomic Status and Hypertension in Korea: the Korean Genome and Epidemiology Study.

    PubMed

    Park, Chan Soon; Ha, Kyoung Hwa; Kim, Hyeon Chang; Park, Sungha; Ihm, Sang Hyun; Lee, Hae Young

    2016-12-01

    We investigated the association between socioeconomic status and hypertension in Korea, a country that has experienced a dynamic socioeconomic transition. We analyzed participants of a prospective cohort study-the Korean Genome and Epidemiology Study-enrolled between 2001 and 2003. We recruited 7,089 subjects who underwent a 4-year follow up till 2007. Education and income levels, which are important parameters for socioeconomic status, were stratified into 4 groups. Education level was defined as short (≤ 6 years), mid-short (7-9 years), mid-long (10-12 years), and long (≥ 12 years). Monthly income level was stratified as low (< 500,000 KRW), mid-low (500,000-1,499,999 KRW), mid-high (1,500,000-2,999,999 KRW) or high (≥ 3,000,000 KRW). At baseline, 2,805 subjects (39.5%) were diagnosed with hypertension. Education and income levels were inversely associated with the prevalence and incidence of hypertension (P < 0.001). In multivariate analysis, a shorter duration of education was significantly associated with a higher prevalence of hypertension (P < 0.001), but income level was not (P = 0.305). During the follow-up, 605 subjects (14.2%) were newly diagnosed with hypertension. In multivariate adjusted analysis, the hazard ratios (95% confidence interval) for incident hypertension across the longer education groups were 0.749 (0.544-1.032), 0.639 (0.462-0.884), and 0.583 (0.387-0.879), compared with the shortest education group. There was no significant association between incident hypertension and income across higher income groups: 0.988 (0.714-1.366), 0.780 (0.542-1.121), and 0.693 (0.454-1.056), compared with the lowest income group. In conclusion, education and income levels are associated with the prevalence and incidence of hypertension, but only education is an independent prognostic factor in Korea.

  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. Lung Cancer Epidemiology in Korea.

    PubMed

    Shin, Aesun; Oh, Chang-Mo; Kim, Byung-Woo; Woo, Hyeongtaek; Won, Young-Joo; Lee, Jin-Soo

    2017-07-01

    The current study was undertaken to examine the trends in the lung cancer incidence, mortality, and survival after a diagnosis in Korea. Lung cancer incidence data according to the histologic type and mortality data were obtained from the Korea Central Cancer Registry and the Statistics Korea, respectively. The age-standardized incidence and mortality rates were calculated, and the Joinpoint model and age-period-cohort analyses were used to describe the trends in the rates. The 5-year relative survival rates of lung cancer were also calculated. Although the number of new lung cancer cases increased between 1999 and 2012, the age-standardized incidence rate decreased by 0.9% per year in men, whereas the incidence in women increased by 1.7% per year over the same time. Until 2010, the most common histologic type in men was squamous cell carcinoma, then adenocarcinoma prevailed thereafter. Since 1999, the most frequent histological type in women was adenocarcinoma. The lung cancer mortality started to decrease in 2002, with a more apparent decline for the younger age groups in both men and women. Overall, the 5-year relative survival rates have improved significantly from 11.2% for men and 14.7% for women among patients diagnosed between 1993 and 1997 to 19.3% for men and 28.2% for women among patients diagnosed between 2008 and 2012, respectively. An improvement in survival rate was observed for all major histology groups. The epidemiology of lung cancer in Korea has changed over a short time span, with decreasing mortality and improving survival rates. Further study is warranted to determine the cause of these changes.

  5. 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.

  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. Epidemiology of Biliary Atresia in Korea

    PubMed Central

    2017-01-01

    Biliary atresia (BA) is the major cause of cholestasis and the leading indication for liver transplantation (LT). However, the incidence of BA in Korea has not been reported. The aim of this study was to investigate the incidence and clinical outcomes of BA in Korea. We used the Korean universal health insurance database and extracted data regarding BA patients younger than 18 years of age admitted between 2011 and 2015. The incidence of BA was calculated by dividing the number of BA patients by the number of live births. Two hundred forty infants were newly diagnosed with BA. A total of 963 BA patients younger than 18 years of age were followed up for 5 years. The overall incidence of BA was 1.06 cases per 10,000 live births. The incidence of BA was 1.4 times higher for female patients than for male patients. Additionally, significant seasonal variation was observed; in particular, the incidence of BA was 2 times higher from June through August than from December through February. Congenital anomalies were found in 38 of 240 patients (15.8%). Congenital heart diseases were major associated congenital anomalies (6.3%). Several complications developed during the study period, including cholangitis (24.0%), varix (6.2%), and gastrointestinal bleeding (4.4%). Three hundred and one of the 963 BA patients under 18 years of age (31.3%) received LT for BA. The incidence of BA is higher in Korea than that in Western countries. We also report significant gender-associated differences and seasonal variation with respect to the incidence of BA. PMID:28244293

  8. Spatial epidemiology of dry eye disease: findings from South Korea.

    PubMed

    Um, Sun-Bi; Kim, Na Hyun; Lee, Hyung Keun; Song, Jong Suk; Kim, Hyeon Chang

    2014-08-15

    DED rate maps from diverse regions may allow us to understand world-wide spreading pattern of the disease. Only few studies compared the prevalence of DED between geographical regions in non-spatial context. Therefore, we examined the spatial epidemiological pattern of DED prevalence in South Korea using a nationally representative sample. We analyzed 16,431 Korean adults aged 30 years or older of the 5th Korea National Health and Nutrition Examination Survey. DED was defined as previously diagnosed by an ophthalmologist as well as symptoms experienced. Multiple logistic regression analysis was used to assess the spatial pattern in the prevalence of DED, and effects of environmental factors. Among seven metropolitan cities and nine provinces, three metropolitan cities located in the southeast of Korea revealed the highest prevalence of DED. After adjusting for sex, age and survey year, people living in urban areas had higher risk of having DED. Adjusted odds ratio for having previously diagnosed DED was 1.677 (95% CI 1.299-2.166) for metropolitan cities and 1.580 (95% CI 1.215-2.055) for other cities compared to rural areas. Corresponding odds ratio for presenting DED symptoms was 1.388 (95% CI 1.090-1.766) for metropolitan cities and 1.271 (95% CI 0.999-1.617) for other cities. Lower humidity and longer sunshine duration were significantly associated with DED. Among air pollutants, SO2 was associated with DED, while NO2, O3, CO, and PM10 were not. Our findings suggest that prevalence of DED can be affected by the degree of urbanization and environmental factors such as humidity and sunshine duration.

  9. 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

  10. Epidemiologic survey of head and neck cancers in Korea.

    PubMed

    Kim, Kwang-Moon; Kim, Young Mo; Shim, Yoon-Sang; Kim, Kwang Hyun; Chang, Hyuck Soon; Choi, Jong Ouck; Rho, Young Soo; Kim, Min-Sik; Choi, Eun Chang; Choi, Geon; Sung, Myung-Whun; Kim, Sang-Yun; Lee, Yong-Sik; Baek, Jung-Hwan; Kim, Sang-Hyun; Kim, Young-Ho; Im, Jung-Hyuk; Choi, Sang-Hak; Kim, Jae-Hee

    2003-02-01

    Head and neck cancers have never been systematically studied for clinical purposes yet in Korea. This epidemiological survey on head and neck cancer patients was undertaken from January to December 2001 in 79 otorhinolaryngology resident-training hospitals nationwide. The number of head and neck cancer patients was 1,063 cases in the year. The largest proportion of cases arose in the larynx, as many as 488 cases, which accounted for 45.9%. It was followed by, in order of frequency, oral cavity (16.5%), oropharynx (10.0%), and hypopharynx (9.5%). The male:female ratio was 5:1, and the mean age was 60.3 yr. Surgery was the predominant treatment modality in head and neck cancers: 204 (21.5%) cases were treated with only surgery, 198 (20.8%) cases were treated with surgery and radiotherapy, 207 cases (21.8%) were treated with combined therapy of surgery, radiotherapy, and chemotherapy. Larynx and hypopharynx cancers had a stronger relationship with smoking and alcohol drinking than other primary site cancers. Of them, 21 cases were found to be metastasized at the time of diagnosis into the lung, gastrointestinal tract, bone, or brain. Coexisting second primary malignancies were found in 23 cases. At the time of diagnosis, a total of 354 cases had cervical lymph node metastasis accounting for 42.0%.

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

    PubMed

    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

    2016-06-01

    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. 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. 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 outbreaks of hantavirus infection.

  12. 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.

  13. [Epidemiological characteristics of Middle East Respiratory Syndrome outbreak in the Republic of Korea, 2015].

    PubMed

    Xiang, Nijuan; Lin, Dan; An, Guangxu; Sui, Haitian; Yang, Zhiyong; Li, Dan; Zhao, Jian; Ma, Tao; Wang, Yali; Ren, Ruiqi; Zhang, Xinyan; Ni, Daxin; Zhang, Yanping; Li, Qun

    2015-08-01

    To analyze the epidemiological characteristics of Middle East Respiratory Syndrome (MERS) outbreak in the Republic of Korea in 2015 and provide related information for the public health professionals in China. The incidence data of MERS were collected from the websites of the Korean government, WHO and authoritative media in Korea for this epidemiological analysis. Between May 20 and July 13, 2015, a total of 186 confirmed MERS cases (1 index case, 29 secondary cases, 125 third generation cases, 25 fourth generation cases and 6 cases without clear generation data), including 36 deaths (case fatality rate: 19%), were reported in Korea. All cases were associated with nosocomial transmission except the index case and two possible family infections. Sixteen hospitals in 11 districts in 5 provinces/municipalities in Korea reported confirmed MERS cases, involving 39 medical professionals or staff. For the confirmed cases and death cases, the median ages were 55 years and 70 years respectively, and the cases and deaths in males accounted for 60% and 67% respectively. Up to 78% of the deaths were with underlying medical conditions. Besides the index case, other 12 patients were reported to cause secondary cases, in which 1 caused 84 infections. One imported MERS case from Korea was confirmed in China on May 29, no secondary cases occurred. The viruses strains isolated from the cases in Korea and the imported case in China show no significant variation compared with the strains isolated in the Middle East. The epidemiological pattern of the MERS outbreak in Korea was similar to MERS outbreaks occurred in the Middle East.

  14. Mitochondrial genomic comparison of Clonorchis sinensis from South Korea with other isolates of this species.

    PubMed

    Wang, Daxi; Young, Neil D; Koehler, Anson V; Tan, Patrick; Sohn, Woon-Mok; Korhonen, Pasi K; Gasser, Robin B

    2017-02-22

    Clonorchiasis is a neglected tropical disease that affects >35 million people mainly in China, Vietnam, South Korea and some parts of Russia. The disease-causing agent, Clonorchis sinensis, is a liver fluke of humans and other piscivorous animals, and has a complex aquatic life cycle involving snails and fish intermediate hosts. Chronic infection in humans causes liver disease and associated complications including malignant bile duct cancer. Central to control and to understanding the epidemiology of this disease is knowledge of the specific identity of the causative agent as well as genetic variation within and among populations of this parasite. Although most published molecular studies seem to suggest that C. sinensis represents a single species and that genetic variation within the species is limited, karyotypic variation within C. sinensis among China, Korea (2n=56) and Russian Far East (2n=14) suggests that this taxon might contain sibling species. Here, we assessed and applied a deep sequencing-bioinformatic approach to sequence and define a reference mitochondrial (mt) genome for a particular isolate of C. sinensis from Korea (Cs-k2), to confirm its specific identity, and compared this mt genome with homologous data sets available for this species. Comparative analyses revealed consistency in the number and structure of genes as well as in the lengths of protein-coding genes, and limited genetic variation among isolates of C. sinensis. Phylogenetic analyses of amino acid sequences predicted from mt genes showed that representatives of C. sinensis clustered together, with absolute nodal support, to the exclusion of other liver fluke representatives, but sub-structuring within C. sinensis was not well supported. The plan now is to proceed with the sequencing, assembly and annotation of a high quality draft nuclear genome of this defined isolate (Cs-k2) as a basis for a detailed investigation of molecular variation within C. sinensis from disparate

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

    PubMed

    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.

  20. Epidemiology and clinical features of HIV infection/AIDS in Korea.

    PubMed

    Kim, June Myung; Cho, Goon Jae; Hong, Sung Kwan; Chang, Kyung Hee; Chung, Joo Sup; Choi, Young Hwa; Song, Young Goo; Huh, Aejung; Yeom, Joon Sup; Lee, Kkot Sil; Choi, Jun Yong

    2003-06-30

    HIV infection/AIDS shows characteristic epidemiological and clinical patterns according to the region, country, and race. The epidemiological and clinical patterns of HIV infection/ AIDS in Korea was investigated by retrospectively analyzing the medical records of 176 HIV-infected persons who visited two major referral hospitals of AIDS in Korea from 1985 to April 2000. The most common transmission route was heterosexual contact (52.3%), followed by homosexual contact (23.9%). Among the opportunistic diseases, candidiasis was the most prevalent (21.6%), followed by Pneumocystis carinii pneumonia (15.9%), tuberculosis (12.5%), and CMV infection (9.1%). The most common initial AIDS-defining opportunistic disease was tuberculosis (33.3%). The most common causes of death were tuberculosis (25.7%) and Pneumocystis carinii pneumonia (25.7%). This study describes the epidemiological and clinical patterns of HIV infection/AIDS in Korea, which not only enables us to accurately understand HIV infection/ AIDS in this country, but eventually to aid in establishing effective preventive measures and treatment guidelines in Korea.

  1. Complete genome sequence of Vibrio parahaemolyticus strain FORC_008, a foodborne pathogen from a flounder fish in South Korea.

    PubMed

    Kim, Suyeon; Chung, Han Young; Lee, Dong-Hoon; Lim, Jong Gyu; Kim, Se Keun; Ku, Hye-Jin; Kim, You-Tae; Kim, Heebal; Ryu, Sangryeol; Lee, Ju-Hoon; Choi, Sang Ho

    2016-07-01

    Vibrio parahaemolyticus is a Gram-negative, motile, nonspore-forming pathogen that causes foodborne illness associated with the consumption of contaminated seafoods. Although many cases of foodborne outbreaks caused by V. parahaemolyticus have been reported, the genomes of only five strains have been completely sequenced and analyzed using bioinformatics. In order to characterize overall virulence factors and pathogenesis of V. parahaemolyticus associated with foodborne outbreak in South Korea, a new strain FORC_008 was isolated from flounder fish and its genome was completely sequenced. The genomic analysis revealed that the genome of FORC_008 consists of two circular DNA chromosomes of 3266 132 bp (chromosome I) and 1772 036 bp (chromosome II) with a GC content of 45.36% and 45.53%, respectively. The entire genome contains 4494 predicted open reading frames, 129 tRNAs and 31 rRNA genes. While the strain FORC_008 does not have genes encoding thermostable direct hemolysin (TDH) and TDH-related hemolysin (TRH), its genome encodes many other virulence factors including hemolysins, pathogenesis-associated secretion systems and iron acquisition systems, suggesting that it may be a potential pathogen. This report provides an extended understanding on V. parahaemolyticus in genomic level and would be helpful for rapid detection, epidemiological investigation and prevention of foodborne outbreak in South Korea.

  2. Epidemiological features and clinical manifestations of Lyme borreliosis in Korea during the period 2005-2012.

    PubMed

    Moon, Shinje; Hong, Yeongseon; Hwang, Kyu-Jam; Kim, Suyeon; Eom, Jihye; Kwon, Donghyok; Park, Ji-Hyuk; Youn, Seung-Ki; Sohn, Aeree

    2015-01-01

    Lyme borreliosis is one of the most common tick-borne infections in the northern hemisphere. However, the epidemiological features and clinical manifestations of this disease in Korea are unknown. The present study is the first to investigate the characteristics of Lyme borreliosis in Korea. We traced suspected cases of Lyme borreliosis during the period 2005-2012. Of the 16 identified patients with the disease, 11 had acquired autochthonous infection within Korea, while 5 patients were infected outside Korea. The history of past exposure was investigated in 8 of the 11 patients with autochthonous infection; 5 of these 8 patients (62.5%) were suspected to have acquired the infection in the northeastern alpine region. Clinically, of 11 patients with autochthonous infection, 6 (54.5%) showed early skin manifestations, 4 (36.4%) showed neurological manifestations, and 1 (9.1%) showed acrodermatitis chronica atrophicans. In conclusion, Lyme borreliosis could be endemic in the northeastern alpine region of Korea, and neurological and early skin manifestations are likely to be the major clinical characteristics of autochthonous Lyme borreliosis in Korea.

  3. Molecular epidemiology of bovine noroviruses in South Korea.

    PubMed

    Park, Sang-Ik; Jeong, Cheol; Kim, Ha-Hyun; Park, Sung-Hee; Park, Su-Jin; Hyun, Bang-Hun; Yang, Dong-Kun; Kim, Sang-Ki; Kang, Mun-Il; Cho, Kyoung-Oh

    2007-09-20

    Since the prevalence of bovine norovirus (BNoV) and their genetic diversity have only been reported in the USA, England, Germany and The Netherlands, this study examined the prevalence and genetic diversity of BNoVs in diarrheic calves in South Korea using 645 diarrheic fecal specimens from calves by RT-PCR and nested PCR assays. Overall, 9.3% of the diarrheic fecal samples tested positive for BNoVs by either RT-PCR or nested PCR, of which 5.9% samples also tested positive for other enteric pathogens including the bovine coronavirus, bovine viral diarrhea virus, bovine torovirus, bovine groups A, B and C rotaviruses, bovine enteric Nebraska-like calicivirus and Escherichia coli. The genetic diversity was determined by direct sequencing of the partial RdRp region of 12 BNoVs detected from the fecal samples by nested PCR. Among the BNoVs examined, one Korean BNoV strain had the highest nucleotide (86.8%) and amino acid (99.1%) identity with the genotype 1 BNoV (GIII-1) strain, while the remaining 11 Korean BNoVs shared a higher nucleotide (88.0-90.5%) and amino acid (93.5-99.1%) identity with the genotype 2 BNoV (GIII-2) strains. The phylogenetic data for the nucleotide and amino acid sequences also demonstrated that one Korean BNoV strain clustered with GIII-1 but the remaining eleven strains clustered with GIII-2. In conclusion, BNoV infections are endemic and there are two distinct genotypes with GIII-2 being the main genotype circulating in the calf population in South Korea.

  4. 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.

  5. Molecular epidemiology of bovine toroviruses circulating in South Korea.

    PubMed

    Park, Su-Jin; Oh, Eun-Hee; Park, Sang-Ik; Kim, Ha-Hyun; Jeong, Young-Ju; Lim, Guem-Ki; Hyun, Bang-Hun; Cho, Kyoung-Oh

    2008-01-25

    The prevalence of the bovine torovirus (BToV) and its genetic characterization have been reported in North America, Europe and Japan. Therefore, this study examined the prevalence and genetic diversity of the BToV in a total of 645 diarrheic fecal samples from 629 Korean native beef calf herds using RT-PCR and nested PCR with the primer pairs specific to a part of the BToV membrane (M) gene. Overall, 19 (2.9%) out of 645 diarrheic samples from 19 herds (6.9%) tested positive for BToVs by either RT-PCR or nested PCR. A comparison of the nucleotide (nt) and amino acid (aa) sequences of a part of the BToV M gene (409bp) among the BToVs showed the Korean BToVs to have comparatively higher sequence homology to the Japanese and Dutch BToVs than to the American and Italian BToVs. Generally, the Korean BToV strains clustered with the Japanese and Dutch BToV strains. However, the American and Italian BToV strains clustered on a separate major branch, suggesting that these are more distantly related to other known BToV strains. These results suggest that the BToV infections are sporadic in diarrheic calves in South Korea, and the Korean BToV strains are more closely related to the Japanese and Dutch BToVs than to the American and Italian BToVs.

  6. 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.

  7. 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

  8. Epidemiological Investigation of an Outbreak of Salmonellosis in Gyeongju, Korea

    PubMed Central

    Yoo, Seok-Ju; Lee, Kwan

    2014-01-01

    Objectives A salmonellosis outbreak occurred within a community of Gyeongju residents who ingested catered food from a wedding in June 2009. We aimed to epidemiologically investigate the probable vehicle of the infection. Methods We conducted a retrospective cohort study on 34 local residents who ingested the wedding food. Results Among the 34 residents, 31 (91.2%) reported symptoms of infection after eating the food. Among all of the wedding foods, pan-fried foods were highly associated with the diarrheal attack rate. On bacteriological examination, Salmonella species were detected in the pan-fried foods among the leftover foods and in 17 of the 31 stool specimens from the cases. There were five different types of pan-fried foods, but the onset of symptoms was independent of the ingredients used. We found that the pan-fried food was prepared at a food store in Seoul and that eggs were a common ingredient. Conclusions The major cause of the salmonellosis in this population was presumed to be the pan-fried food prepared with contaminated eggs. These food items might have been partially undercooked because of their irregular shape, which allowed the Salmonella species to survive and multiply before ingestion. PMID:24921021

  9. Epidemiological investigation of an outbreak of salmonellosis in Gyeongju, Korea.

    PubMed

    Yoo, Seok-Ju; Lim, Hyun-Sul; Lee, Kwan

    2014-05-01

    A salmonellosis outbreak occurred within a community of Gyeongju residents who ingested catered food from a wedding in June 2009. We aimed to epidemiologically investigate the probable vehicle of the infection. We conducted a retrospective cohort study on 34 local residents who ingested the wedding food. Among the 34 residents, 31 (91.2%) reported symptoms of infection after eating the food. Among all of the wedding foods, pan-fried foods were highly associated with the diarrheal attack rate. On bacteriological examination, Salmonella species were detected in the pan-fried foods among the leftover foods and in 17 of the 31 stool specimens from the cases. There were five different types of pan-fried foods, but the onset of symptoms was independent of the ingredients used. We found that the pan-fried food was prepared at a food store in Seoul and that eggs were a common ingredient. The major cause of the salmonellosis in this population was presumed to be the pan-fried food prepared with contaminated eggs. These food items might have been partially undercooked because of their irregular shape, which allowed the Salmonella species to survive and multiply before ingestion.

  10. A global network for investigating the genomic epidemiology of malaria

    PubMed Central

    2013-01-01

    Large-scale studies of genomic variation could assist efforts to eliminate malaria. But there are scientific, ethical and practical challenges to carrying out such studies in developing countries, where the burden of disease is greatest. The Malaria Genomic Epidemiology Network (MalariaGEN) is now working to overcome these obstacles, using a consortial approach that brings together researchers from 21 countries. PMID:19079050

  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. Epidemiological Characteristics of the First Water-Borne Outbreak of Cryptosporidiosis in Seoul, Korea

    PubMed Central

    Moon, Shinje; Kwak, Wooseok; Lee, Sangwon; Kim, Won; Oh, Jaeyeon

    2013-01-01

    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. PMID:23853479

  13. Molecular typing for epidemiological evaluation of Brucella abortus and Brucella canis isolated in Korea.

    PubMed

    Kang, Sung-Il; Her, Moon; Heo, Eun Jeong; Nam, Hyang Mi; Jung, Suk Chan; Cho, Donghee

    2009-08-01

    To investigate genotype relationships among regional groups of Brucella isolates, variable-number tandem-repeat (VNTR) analysis was conducted according to previously reported methods. Field strains of Brucella abortus and Brucella canis were isolated from 9 provinces in the Republic of Korea during the years 1996-2006 and each of the isolates was classified by eight loci of HOOF-Prints. On the basis of the alleles, the 33 B. abortus and 21 B. canis field strains were divided into 22 and 18 distinct genotypes, respectively. Phylogenetic cluster analysis of Brucella isolates could be discriminated with geographical region in the Republic of Korea. Simpson's diversity index values of B. abortus and B. canis isolates ranged from 0 to 0.85. The stability of each locus was determined with in vivo and in vitro experiments. After twenty passages in blood agar, the VNTR numbers of loci 1 and 7 in B. abortus isolates and loci 5, 7, and 8 in B. canis isolates changed. The same change of the VNTR numbers at loci 1 and 7 was observed with B. abortus RB51 strains isolated from vaccinated cattle for the in vivo experiment. Although B. canis and B. abortus isolates were discriminated to herd levels by the HOOF-Prints, this method needs further improvement for the high variable locus. This study represents the first epidemiological data of molecular typing of B. abortus and B. canis reported in Korea.

  14. Ten-year analysis of adenovirus type 7 molecular epidemiology in Korea, 1995-2004: implication of fiber diversity.

    PubMed

    Choi, Eun Hwa; Lee, Hoan Jong; Kim, Sun Jung; Eun, Byung Wook; Kim, Nam Hee; Lee, Jin A; Lee, Jun Ho; Song, Eun Kyung; Kim, So Hee

    2006-04-01

    Adenovirus type 7 (Ad7) is frequently responsible for severe respiratory infections, especially in young infants. Since the Ad7 epidemics have been associated with severe childhood pneumonia and significant mortality in Korea, 1995-1999, continuous surveillance was necessary for Ad7 related diseases. To characterize epidemiologic features of Ad7 in 1995-2004, genetic diversity of Ad7 were studied by determining genome types (GTs) and the fiber diversity. A total of 139 Ad7 strains were obtained from Korean children with pneumonia. Serotype specificity was confirmed by microneutralization assay. GTs were determined by restriction analysis with 12 enzymes. The variable region of the fiber was sequenced. Two GTs, Ad7d (N=98, 71%) and Ad7l (N=41, 29%) have been identified. In 1995-1996 and 2001-2002, Ad7d was dominant accounting for 98-100% of all Ad7; in 1999-2000, Ad7l was the prevalent GT accounting for 100% of all Ad7; in 1997-1998 and 2003-2004, both GTs circulated concurrently. The change in the relative predominance of GT occurred in 2 or 3 years. The Lys substitution for Arg at codon 280 of the fiber was identified in 31 Ad7d strains (32%) while no variations were observed among Ad7l. It was noteworthy that two fiber variants of Ad7d were not concurrently prevalent on any time after 1996. The shift in predominant fiber variants of Ad7d was also observed in 2-3 years. Our data demonstrated that the two GTs, Ad7d and Ad7l circulated in an alternating manner between outbreaks of Ad7 associated childhood pneumonia over 10 consecutive years in Korea. Fiber diversity at position 280 within Ad7d appeared to contribute to the annual distribution of Ad7d. This observation necessitates further studies to demonstrate an association between fiber variation and host cell specificity or neutralization antibody recognition.

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

    PubMed

    Lee, Won-Chang; Kwon, Young Hwan

    2016-05-01

    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. 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. 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. 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.

  16. 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

  17. Infection control in the new age of genomic epidemiology.

    PubMed

    Tang, Patrick; Croxen, Matthew A; Hasan, Mohammad R; Hsiao, William W L; Hoang, Linda M

    2017-02-01

    With the growing importance of infectious diseases in health care and communicable disease outbreaks garnering increasing attention, new technologies are playing a greater role in helping us prevent health care-associated infections and provide optimal public health. The microbiology laboratory has always played a large role in infection control by providing tools to identify, characterize, and track pathogens. Recently, advances in DNA sequencing technology have ushered in a new era of genomic epidemiology, where traditional molecular diagnostics and genotyping methods are being enhanced and even replaced by genomics-based methods to aid epidemiologic investigations of communicable diseases. The ability to analyze and compare entire pathogen genomes has allowed for unprecedented resolution into how and why infectious diseases spread. As these genomics-based methods continue to improve in speed, cost, and accuracy, they will be increasingly used to inform and guide infection control and public health practices.

  18. Epidemiologic Impact of Rapid Industrialization on Head Injury Based on Traffic Accident Statistics in Korea

    PubMed Central

    Chung, You Nam; Park, Young Seok; Min, Kyung Soo; Lee, Mou Seop; Kim, Young Gyu

    2016-01-01

    Objective The aim of the present study is to estimate the incidence trend of head injury and the mortality based on traffic accident statistics and to investigate the impacts of rapid industrialization and economic growth on epidemiology of head injury in Korea over the period 1970–2012 including both pre-industrialized and post-industrialized stages. Methods We collected data of head injury estimated from traffic accident statistics and seven hospital based reports to see incidence trends between 1970 and 2012. We also investigated the population structure and Gross National Income (GNI) per capita of Korea over the same period. The age specific data were investigated from 1992 to 2012. Results The incidence of head injury gradually rose in the 1970s and the 1980s but stabilized until the 1990s with transient rise and then started to decline slowly in the 2000s. The mortality grew until 1991 but gradually declined ever since. However, the old age groups showed rather slight increase in both rates. The degree of decrease in the mortality has been more rapid than the incidence on head injury. Conclusion In Korea during the low income stage, rapid industrialization cause considerable increase in the mortality and the incidence of head injury. During the high income stage, the incidence of head injury gradually declined and the mortality dropped more rapidly than the incidence due to preventive measures and satisfactory medical care. Nevertheless, the old age groups revealed rather slight increase in both rates owing to the large population structure and the declining birth rate. PMID:26962421

  19. 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.

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

    PubMed Central

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

    2015-01-01

    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. PMID:26539007

  1. Epidemiology and Clinical Characteristics of Zika Virus Infections Imported into Korea from March to October 2016.

    PubMed

    Yoon, Doran; Shin, Seung Hwan; Jang, Hee Chang; Kim, Eu Suk; Song, Eun Hee; Moon, Song Mi; Shin, So Youn; Choe, Pyeong Gyun; Sung, Jung Joon; Choi, Eun Hwa; Oh, Myoung Don; Jee, Youngmee; Kim, Nam Joong

    2017-09-01

    Zika is a re-emerging, mosquito-borne viral infection, which has been recently shown to cause microcephaly and Guillain-Barré syndrome. Since 2015 the number of infected patients has increased significantly in South America. The purpose of this study was to identify the epidemiologic and clinical characteristics of patients with Zika virus (ZIKV) infections in Korea. Patients who had visited areas of risk and tested positive in the ZIKV reverse transcriptase polymerase chain reaction (RT-PCR) in blood, urine, or saliva specimens were included. The first Korean case of ZIKV infection was reported in March 2016, and 14 cases had been reported by October 2016. The median age of the patients was 34 years (19-64 years). Ten patients had been exposed in Southeast Asia and 4 in Latin America. Rash was the most common symptom (92.9%; 13/14), followed by myalgia (50.0%; 7/14), and arthralgia (28.6%, 4/14). There were no neurologic abnormalities and none of the patients was pregnant. Results of biochemical tests were normal. Positivity rates of RT-PCR for ZIKV in serum, urine, and saliva were 53.8%, 100.0%, and 83.3%, respectively in the first week of symptoms. In conclusion, 14 patients with ZIKV infections were reported in Korea by October 2016 and all of them had mild clinical symptoms. © 2017 The Korean Academy of Medical Sciences.

  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.

  4. 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

  5. Epidemiological study of erythromycin-resistant Streptococcus pyogenes from Korea and Japan by emm genotyping and multilocus sequence typing.

    PubMed

    Takahashi, Takashi; Arai, Kazuaki; Lee, Dong Hyun; Koh, Eun Ha; Yoshida, Haruno; Yano, Hisakazu; Kaku, Mitsuo; Kim, Sunjoo

    2016-01-01

    We determined the epidemiological characteristics of erythromycin (EM)-resistant Streptococcus pyogenes (group A streptococci, GAS) strains isolated from Korea and Japan, using emm genotyping and multilocus sequence typing (MLST). Clinical isolates of GAS had been collected from 1992 to 2012 in Korea and from 2004 to 2009 in Japan. EM resistance was determined by the microdilution method, and resistance genotypes were assessed by PCR. The emm genotyping and MLST were performed by DNA sequencing. The emm genotypes and sequence types (STs) were concordant in 143 (85.1%) of 168 EM-resistant GAS strains from Korea. ST36/emm12 (35.1%), ST52/emm28 (22.6%), and ST49/emm75 (16.1%) were the most common types. Most of the ST36 (93.9%) and ST52 (95.8%) strains harbored erm(B), whereas strains ST49, ST42, and ST15 contained mef(A). The concordance between emm genotypes and STs was 41 (93.2%) among 44 EM-resistant GAS strains from Japan. ST36/emm12 (34.1%), ST49/emm75 (18.2%), and ST28/emm1 (15.9%) were the major types. ST36 isolates harbored either erm(B) (56.3%) or mef(A) (37.5%), whereas isolates ST28, ST49, and ST38 carried only mef(A). The proportion of erm(B) and mef(A) was 66.1% and 33.3% in Korea and 22.7% and 68.2% in Japan, respectively. The common STs in Korea and Japan were ST36 and ST49, whereas ST52 was present only in Korea and ST28 only in Japan. Genotype erm(B) was predominant in Korea, whereas mef(A) was frequent in Japan. There were differences between Korea and Japan regarding the frequencies of emm genotypes, STs, and EM resistance genes among the EM-resistant GAS.

  6. 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

  7. Epidemiology and Clinical Features of Kawasaki Disease in South Korea, 2012-2014.

    PubMed

    Kim, Gi Beom; Park, Sohee; Eun, Lucy Youngmin; Han, Ji Whan; Lee, Soo Young; Yoon, Kyung Lim; Yu, Jeong Jin; Choi, Jong-Woon; Lee, Kyung-Yil

    2017-05-01

    To reveal the recent epidemiologic features of Kawasaki disease (KD) in South Korea based on data from a nationwide survey. We collected data between 2012 and 2014 regarding the incidence, symptoms and signs, treatment trends and coronary complications associated with acute KD by sending questionnaires to 97 hospitals with pediatric residency programs as well as 19 community hospitals without residency training. We received full and partial data from 97 and 13 hospitals, respectively (response rate: 94.8%). A total of 14,916 cases of KD were reported by these 110 hospitals (4588 in 2012, 5183 in 2013 and 5145 in 2014). The male-to-female ratio was 1.4:1, and the median age at diagnosis was 29 months. The incidence of KD per 100,000 children younger than 5 years of age were 170.9, 194.9 and 194.7 in 2012, 2013 and 2014, respectively. The recurrence rate was 4.7%. KD occurred more frequently during summer (especially June and July) and winter (December and January) seasons. Intravenous immunoglobulin was administered to 95.4% of the patients, and the nonresponder rate for the first intravenous immunoglobulin was 11.8%. Coronary aneurysm occurred in 1.7% of the patients, and giant aneurysm developed in 19 patients (0.16%) during the 3 years. One patient had myocardial infarction and 1 patient died of suspected coronary aneurysm rupture. The incidence of KD in South Korea increased to 194.7 per 100,000 children younger than 5 years in 2014; meanwhile, the coronary aneurysm rate decreased to 1.7%.

  8. A Comparative Study of the Epidemiological Aspects of Legionnaires’ Disease: Outbreaks in Korea and Japan, 2010 - 2014

    PubMed Central

    Han, Bok-Soon; Lee, Myeong-Jin; Kwon, Young-Hwan; Lee, Won-Chang

    2017-01-01

    Background In the present study, we compared the epidemiological aspects of Legionnaire’ disease (LD) outbreaks in Korea and Japan by analyzing the current state from 2010 to 2014. Methods The following factors were analyzed: nationwide cumulative incidence rate (CIR) per 100,000 populations and case-fatality rate in percentage, epidemiological aspects (i.e., case related to gender), male to female morbidity ratio (MFMR), age, seasonality and habitat distribution of LD cases. Results In total, there were 134 cases of LD with the CIR of 0.05 per 100,000 populations in Korea from 2010 to 2014. During the same period in Japan, there were 4,840 cases of LD with a CIR of 0.76 per 100,000 populations. The CIR in Japan was significantly higher than that in Korea. However, the case-fatality rates were at similar levels (3.0% vs. 5.9%). Moreover, LD affects both sexes differently, accounting for 2.05 and 4.41 of MFMR in Korea and Japan, respectively. In both countries, the incidence mainly occurred among people aged 40 years or older, and peaked in summer (37.3% vs. 33.7% of total cases). Significant differences were observed in the incidence of LD cases between the capital city and county areas in both two countries. These differences in LD risk factors reflect the different influences of reservoir/host with natural or artificial aquatic environments. Conclusion This study provides a quantitative analysis of the epidemiological aspects and risk factors of LD outbreaks in Korea and Japan. We hope this study would be helpful for providing insight on effective future strategies to reduce LD outbreaks. PMID:27924178

  9. Epidemiological and Clinical Features of Severe Fever with Thrombocytopenia Syndrome during an Outbreak in South Korea, 2013–2015

    PubMed Central

    Park, Sun-Whan; Ryou, Jungsang; Choi, Woo-Young; Han, Myung-Guk; Lee, Won-Ja

    2016-01-01

    Since the first reported case of severe fever with thrombocytopenia syndrome (SFTS) in South Korea in 2013, between 2013 and 2015, we collected 1,697 serum samples from suspected patients who experienced symptoms of SFTS. We performed reverse transcriptase polymerase chain reaction using total RNA extracted from the patients' sera. When viral RNA was detected in the sera, SFTS was diagnosed. Among the 1,697 samples, 170 were positive for SFTS virus. We then analyzed the epidemiologic features of these 170 cases. As a result, we found that the annual number of cases increased steadily. However, the annual case fatality rate exhibited a downward trend. The majority of patients were aged ≥ 60 years, and most cases occurred during May–October in the eastern and southern parts of the country. These results may be useful for effective SFTS control by describing the clinical and epidemiologic features of the disease in South Korea. PMID:27928084

  10. Molecular epidemiologic investigation of lentogenic Newcastle disease virus from domestic birds at live bird markets in Korea.

    PubMed

    Choi, Kang-Seuk; Lee, Eun-Kyoung; Jeon, Woo-Jin; Kwon, Jun-Hun; Lee, Jin-Hwa; Sung, Haan-Woo

    2012-03-01

    A Newcastle disease surveillance program was conducted at live bird markets in Korea to expand our epidemiologic understanding of the disease in Korea. During the surveillance program, 10 lentogenic Newcastle disease viruses (NDVs) were isolated and identified from apparently healthy chickens and ducks at live bird markets. The lentogenic viruses had sequence motifs of either 112GKQGRL117 (n = 8) or 112GRQGRL117 (n = 2) at the F0 cleavage site. Sequencing and phylogenetic analyses of NDV isolates based on the hypervariable region of the F protein revealed two different genotypes: genotypes I (n = 8) and II (n = 2). Genotype I viruses were most closely related to the NDV V4 strain (n = 7) or the NDV Ulster 2C strain (n = 1). In contrast, genotype II viruses clustered with the NDV vaccine strains (LaSota and VG/GA) that are commonly used as live vaccines in Korea. The epidemiologic importance of NDV at live bird markets in Korea is discussed.

  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.

  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. Dissecting malaria biology and epidemiology using population genetics and genomics.

    PubMed

    Auburn, Sarah; Barry, Alyssa E

    2017-02-01

    Molecular approaches have an increasingly recognized utility in surveillance of malaria parasite populations, not only in defining prevalence and incidence with higher sensitivity than traditional methods, but also in monitoring local and regional parasite transmission patterns. In this review, we provide an overview of population genetic and genomic studies of human-infecting Plasmodium species, highlighting recent advances in the field. In accordance with the renewed impetus for malaria eradication, many studies are now using genetic and genomic epidemiology to support local evidence-based intervention strategies. Microsatellite genotyping remains a popular approach for both Plasmodium falciparum and Plasmodium vivax. However, with the increasing availability of whole genome sequencing data enabling effective single nucleotide polymorphism-based panels tailored to a given study question and setting, this approach is gaining popularity. The availability of new reference genomes for Plasmodium malariae and Plasmodium ovale should see a surge in similar molecular studies on these currently neglected species. Genomic studies are revealing new insights into important adaptive mechanisms of the parasite including antimalarial drug resistance. The advent of new methodologies such as selective whole genome amplification for dealing with extensive human DNA in low density field isolates should see genome-wide approaches becoming routine for parasite surveillance once the economic costs outweigh the current cost benefits of targeted approaches. Copyright © 2016. Published by Elsevier Ltd.

  14. A Comparative Study of the Epidemiology of Human Leptospirosis in Korea and Japan between 2006 and 2012.

    PubMed

    Lee, Myeong-Jin; Miki, Shinichiro; Kitagawa, Masahiro; Lee, Won-Chang

    2016-05-20

    We undertook a comparative analysis of the epidemiology of reported human leptospirosis (HL) cases in Korea and Japan. Between 2006 and 2012, the cumulative incidence of HL in Korea was higher than that in Japan (1.26 vs. 0.14 per 100,000 population, respectively), and the total reported cases were 632 and 196, respectively. Significantly more men were infected than women in both Korea (63.0% men, P < 0.01) and Japan (87.8% men, P < 0.01). In both countries, the incidence was highest among those aged 40 years and older (60%), and peaked in autumn (78.5% cases in Korea, and 46.9% cases in Japan). However, Japan exhibited a significantly higher proportion of male cases, a younger age distribution, and less prominent seasonality. A significant difference was observed in the incidence of HL between the capital city and rural areas in Korea, but not in Japan. The differences in agricultural and forestry practices, and the efficacy or wastewater treatment infrastructure might influence the incidence level in rural areas in both countries. The differences between the 2 countries might be because of their unique geographical characteristics and variations in their levels of industrialization.

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

    PubMed Central

    Fu, Songzhe; Octavia, Sophie; Tanaka, Mark M.; Sintchenko, Vitali

    2015-01-01

    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. PMID:26019201

  16. The Epidemiology of Appendicitis and Appendectomy in South Korea: National Registry Data

    PubMed Central

    Lee, Jung Hun; Park, Young Sun; Choi, Joong Sub

    2010-01-01

    Background Appendicitis is one of the most frequent acute surgical conditions of the abdomen, and appendectomy is one of the most commonly performed operations in the world. However, epidemiological data on appendicitis have not been reported for South Korean or East Asian populations. Methods We analyzed the epidemiological features and lifetime risk of appendicitis and appendectomy in South Korea using data collected for the national health insurance database from 2005 through 2007. Results Appendectomy was performed in 59.70% of inpatients diagnosed with appendicitis. The overall incidences of appendicitis, total appendectomy, and perforated appendectomy were 22.71, 13.56, and 2.91 per 10 000 population per year, respectively. The incidence of appendicitis and appendectomy showed clear seasonality, with a peak in summer. The standardized lifetime risks of appendicitis and appendectomy were constant from 2005 through 2007. A life table model suggests that the lifetime risk of appendicitis is 16.33% for males and 16.34% for females, and that the lifetime risk of appendectomy is 9.89% for males and 9.61% for females. Conclusions As compared to results obtained in research on Western populations, appendicitis and appendectomy had a similar perforation rate and seasonality, but a higher overall incidence, in South Koreans. Between 2005 and 2007, the incidence of appendicitis and appendectomy was constant. Overall, an estimated 15 incidental appendectomies are performed to prevent 1 inpatient with suspected appendicitis, and 26 incidental appendectomies are performed to prevent 1 appendectomy. Incidental appendectomy may have greater preventive value in Koreans. PMID:20023368

  17. 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.

  18. 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.

  19. Clinical characteristics of patients with treated epilepsy in Korea: a nationwide epidemiologic study.

    PubMed

    Kim, Dong Wook; Lee, Seo-Young; Chung, Soo-Eun; Cheong, Hae-Kwan; Jung, Ki-Young

    2014-01-01

    Although a number of epidemiologic studies have been conducted on the prevalence and incidence of epilepsy around the world, only a few studies have investigated the clinical characteristics of patients with epilepsy in a population-based sample. The purpose of the present study was to describe the clinical characteristics of treated patients with epilepsy in Korea via a nationwide medical records survey. The study population was obtained through a nationwide database registered to the Health Insurance Review and Assessment service. Patients were recruited from clinics and hospitals in each cluster according to region and referral level by random selection from a preallocated sample of patients. All patients were being treated with antiepileptic drug medication with or without a diagnosis code for epilepsy or seizure between January 2009 and December 2009. Among the 6,436 selected patients, 2,150 met the diagnostic criteria for epilepsy and were included in our survey on the clinical characteristics of patients who were with treated epilepsy. The proportion of male patients with epilepsy in this study was higher (1,226; 57.0%) than that of female patients. In addition, 10.6% of patients were first diagnosed with epilepsy in 2009, and 53.6% of patients experienced at least one seizure over the course of 2009; 78.1% were classified as having localization-related epilepsy, whereas 7.3% were considered to have generalized epilepsy. Thirty-five percent of patients were thus classified as idiopathic or cryptogenic cases. The most common cause of symptomatic epilepsy was trauma (10.0%), followed by stroke (9.6%), central nervous system (CNS) infection (5.7%), and hippocampal sclerosis (4.9%). This is the first nationwide study of the clinical characteristics of treated epilepsy in Korea using a national database validated by medical records survey. The etiologies of epilepsy and epilepsy syndrome classifications were comparable to those previously reported in other

  20. Trends in the epidemiological aspects and mortality of alcoholic liver disease in Korea in the decade between 2000 and 2009.

    PubMed

    Bang, Hyung-Ae; Kwon, Young-Hwan; Lee, Myeong-Jin; Lee, Won-Chang

    2015-02-01

    Alcohol consumption and related alcohol liver disease (ALD) have substantially increased in Korea during the last decade. The objective of this study was to evaluate the trends in the epidemiological aspects and mortality rate (MR) of Korea in the decade between 2000 and 2009. The raw data analyzed in this study were obtained from the website of "the ALD" managed by Korea Center for Disease Control and Prevention (KCDC), Korea Public Health Association (KPHA), and statistics website of Statistics Korea. The data analyses were performed using Excel 2007 statistical software (Microsoft Corp., USA). The amount of alcohol-consumption-per-capita-per-year (ACCY) in Korea was 8.38 L in 2000 and 8.54 L in 2009. The most taken alcoholic beverage was soju, followed by beer. There were a total of 1,403 case-fatalities (CF) with an MR of 2.98 per 100,000 populations of ALD in 2000, while a total of 3,588 CF with an MR of 7.21 in 2009 (P < 0.01). The CF and MR of ALD in males were significantly higher than those in females (P < 0.01). In over 40-year-old age groups, the CF and MR were significantly increased (P < 0.01). Moreover, occupational classification revealed that the mistress/students/jobless (MSJ) were the most risky group. The comparison of overall CF and MR of ALD by six key classifications (International Classification of Diseases (ICD)) showed that alcoholic cirrhosis (229 CF and 16.3%) in 2000 tended to be increased in 2009 (2,803 CF and 78.1%), while alcoholic fibrosis and sclerosis (607 CF and 43.3%) in 2000 significantly decreased in 2009 (120 CF and 3.3%), respectively. ALD is one of the most severe diseases in Korea, as indicated by its high CF and MR in this study. As over-consumption of alcoholic beverages is relatively common in Korea, more efforts should be made toward prevention of ALD by raising awareness of the risk factors of ALD by public health education.

  1. Trends in the Epidemiological Aspects and Mortality of Alcoholic Liver Disease in Korea in the Decade Between 2000 and 2009

    PubMed Central

    Bang, Hyung-Ae; Kwon, Young-Hwan; Lee, Myeong-Jin; Lee, Won-Chang

    2015-01-01

    Background Alcohol consumption and related alcohol liver disease (ALD) have substantially increased in Korea during the last decade. The objective of this study was to evaluate the trends in the epidemiological aspects and mortality rate (MR) of Korea in the decade between 2000 and 2009. Methods The raw data analyzed in this study were obtained from the website of “the ALD” managed by Korea Center for Disease Control and Prevention (KCDC), Korea Public Health Association (KPHA), and statistics website of Statistics Korea. The data analyses were performed using Excel 2007 statistical software (Microsoft Corp., USA). Results The amount of alcohol-consumption-per-capita-per-year (ACCY) in Korea was 8.38 L in 2000 and 8.54 L in 2009. The most taken alcoholic beverage was soju, followed by beer. There were a total of 1,403 case-fatalities (CF) with an MR of 2.98 per 100,000 populations of ALD in 2000, while a total of 3,588 CF with an MR of 7.21 in 2009 (P < 0.01). The CF and MR of ALD in males were significantly higher than those in females (P < 0.01). In over 40-year-old age groups, the CF and MR were significantly increased (P < 0.01). Moreover, occupational classification revealed that the mistress/students/jobless (MSJ) were the most risky group. The comparison of overall CF and MR of ALD by six key classifications (International Classification of Diseases (ICD)) showed that alcoholic cirrhosis (229 CF and 16.3%) in 2000 tended to be increased in 2009 (2,803 CF and 78.1%), while alcoholic fibrosis and sclerosis (607 CF and 43.3%) in 2000 significantly decreased in 2009 (120 CF and 3.3%), respectively. Conclusion ALD is one of the most severe diseases in Korea, as indicated by its high CF and MR in this study. As over-consumption of alcoholic beverages is relatively common in Korea, more efforts should be made toward prevention of ALD by raising awareness of the risk factors of ALD by public health education. PMID:25436025

  2. Laboratory characteristics of recent hepatitis A in Korea: Ongoing epidemiological shift

    PubMed Central

    Moon, Hee Won; Cho, Jin Hee; Hur, Mina; Yun, Yeo-Min; Choe, Won Hyeok; Kwon, So Young; Lee, Chang Hong

    2010-01-01

    AIM: To evaluate seroprevalence of hepatitis A virus (HAV) antibody and investigate demographic, clinical, and laboratory features of recent cases in Korea. METHODS: For the evaluation of hepatitis A seroprevalence, we analyzed the data from 3127 subjects including, healthcare workers and patients who visited Konkuk University Hospital, a secondary referral center, from January to October 2009. The sera with positive IgM were excluded from seroprevalence data for total HAV antibody. We retrospectively reviewed the electronic medical records of 419 patients with HAV, who were diagnosed by the presence of serum IgM antibodies against HAV. All patients presented at Konkuk University Hospital between August 2005 and September 2008. RESULTS: Among 3127 sera tested, 1428 (45.7%) were positive for anti-HAV antibody. The seroprevalence was very low in teenagers or those in their twenties, increased in those in their thirties, and was > 90% in older patients. In children younger than 10 years, seroprevalence was increased again. Most patients with HAV hepatitis were in their twenties and thirties. The γ-glutamyl transpeptidase increased with age and was significantly higher in patients older than 30 years. Indicators of severity, such as decreased albumin and increased bilirubin, were also more prominent in the older age group; however, the leukocyte count was higher and the frequency of leukopenia was lower in younger patients than in older adults. CONCLUSION: There has been an apparent epidemiological shift in HAV seroprevalence and a change in the peak age of HAV hepatitis. This study could provide baseline data of recent hepatitis A in Asia. PMID:20205283

  3. Laboratory characteristics of recent hepatitis A in Korea: ongoing epidemiological shift.

    PubMed

    Moon, Hee Won; Cho, Jin Hee; Hur, Mina; Yun, Yeo-Min; Choe, Won Hyeok; Kwon, So Young; Lee, Chang Hong

    2010-03-07

    To evaluate seroprevalence of hepatitis A virus (HAV) antibody and investigate demographic, clinical, and laboratory features of recent cases in Korea. For the evaluation of hepatitis A seroprevalence, we analyzed the data from 3127 subjects including, healthcare workers and patients who visited Konkuk University Hospital, a secondary referral center, from January to October 2009. The sera with positive IgM were excluded from seroprevalence data for total HAV antibody. We retrospectively reviewed the electronic medical records of 419 patients with HAV, who were diagnosed by the presence of serum IgM antibodies against HAV. All patients presented at Konkuk University Hospital between August 2005 and September 2008. Among 3127 sera tested, 1428 (45.7%) were positive for anti-HAV antibody. The seroprevalence was very low in teenagers or those in their twenties, increased in those in their thirties, and was > 90% in older patients. In children younger than 10 years, seroprevalence was increased again. Most patients with HAV hepatitis were in their twenties and thirties. The gamma-glutamyl transpeptidase increased with age and was significantly higher in patients older than 30 years. Indicators of severity, such as decreased albumin and increased bilirubin, were also more prominent in the older age group; however, the leukocyte count was higher and the frequency of leukopenia was lower in younger patients than in older adults. There has been an apparent epidemiological shift in HAV seroprevalence and a change in the peak age of HAV hepatitis. This study could provide baseline data of recent hepatitis A in Asia.

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

    PubMed

    Jeong, Jae Hoon; Chun, Yeoun Sook; Park, Ki Ho

    2016-04-01

    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.

  5. Draft Genome Sequence of Jiangella alkaliphila KCTC 19222T, Isolated from Cave Soil in Jeju, Republic of Korea.

    PubMed

    Jiao, Jian-Yu; Liu, Lan; Park, Dong-Jin; Kim, Chang-Jin; Xiao, Min; Chen, Jing; Li, Li; Zhong, Jing-Mei; Zhao, Jiao; Li, Wen-Jun

    2015-07-02

    We report the draft genome sequence of Jiangella alkaliphila KCTC 19222(T), isolated from cave soil in Jeju, Republic of Korea. This genome sequence, together with the previously sequenced J. gansuensis strain DSM 44835(T), identified from a desert environmental source, will give us a better understanding of the school of "evolutionary taxonomy."

  6. Draft Genome Sequence of Jiangella alkaliphila KCTC 19222T, Isolated from Cave Soil in Jeju, Republic of Korea

    PubMed Central

    Jiao, Jian-Yu; Liu, Lan; Park, Dong-Jin; Kim, Chang-Jin; Xiao, Min; Chen, Jing; Li, Li; Zhong, Jing-Mei

    2015-01-01

    We report the draft genome sequence of Jiangella alkaliphila KCTC 19222T, isolated from cave soil in Jeju, Republic of Korea. This genome sequence, together with the previously sequenced J. gansuensis strain DSM 44835T, identified from a desert environmental source, will give us a better understanding of the school of “evolutionary taxonomy.” PMID:26139721

  7. Genome Sequence of Salegentibacter salarius KCTC 12974, Isolated from a Marine Solar Saltern of the Yellow Sea in South Korea

    PubMed Central

    Xu, Yongle; Zheng, Qiang; Liu, Yanting; Jiao, Nianzhi

    2016-01-01

    Salegentibacter salarius KCTC 12974 is isolated from a marine solar saltern of the Yellow Sea in South Korea. Here, we report the draft genome sequence of Salegentibacter salarius KCTC 12974. Various glycoside hydrolase genes in even numbers in the genome reflect the ecological adaption of KCTC 12974 to its habitat. PMID:27881540

  8. Phylogenetic and recombination analysis of genomic sequences of PCV2 isolated in Korea.

    PubMed

    Kim, Hye Kwon; Luo, Yuzi; Moon, Hyung Joon; Park, Seong Jun; Keum, Hyun Ok; Rho, Semi; Park, Bong Kyun

    2009-12-01

    The complete genomic sequences of 13 PCV2 viruses obtained between 2005 and 2007 were analyzed in order to determine their phylogenetic relationship and identify possible recombination events between PCV2a and PCV2b. Twelve PCV2b viruses and one PCV2a virus were identified by phylogenetic analysis. Notably, two PCV2b viruses (PF163 and C7201-1) were shown to belong to the 1B subgroup of PCV2b, which had not been previously reported in Korea. Theses two viruses were also predicted to be possible recombinants between PCV2a (the minor parent) and PCV2b (the major parent) by the RDP program (P < 0.01). A recombination site was predicted to exist in ORF1 of both viruses. This additional evidence of PCV2 recombination in Korea further supports the important role of recombination in genetic evolution.

  9. Genomic and epidemiological characteristics provide new insights into the phylogeographical and spatiotemporal spread of porcine epidemic diarrhea virus in Asia.

    PubMed

    Sun, Min; Ma, Jiale; Wang, Yanan; Wang, Ming; Song, Wenchao; Zhang, Wei; Lu, Chengping; Yao, Huochun

    2015-05-01

    Porcine epidemic diarrhea has become pandemic in the Asian pig-breeding industry, causing significant economic loss. In the present study, 11 complete genomes of porcine epidemic diarrhea virus (PEDV) field isolates from China were determined and analyzed. Frequently occurring mutations were observed, which suggested that full understanding of the genomic and epidemiological characteristics is critical in the fight against PEDV epidemics. Comparative analysis of 49 available genomes clustered the PEDV strains into pandemic (PX) and classical (CX) groups and identified four hypervariable regions (V1 to V4). Further study indicated key roles for the spike (S) gene and the V2 region in distinguishing between the PX and CX groups and for studying genetic evolution. Genotyping and phylogeny-based geographical dissection based on 219 S genes revealed the complexity and severity of PEDV epidemics in Asia. Many subgroups have formed, with a wide array of mutations in different countries, leading to the outbreak of PEDV in Asia. Spatiotemporal reconstruction based on the analysis suggested that the pandemic group strains originated from South Korea and then extended into Japan, Thailand, and China. However, the novel pandemic strains in South Korea that appeared after 2013 may have originated from a Chinese variant. Thus, the serious PED epidemics in China and South Korea in recent years were caused by the complex subgroups of PEDV. The data in this study have important implications for understanding the ongoing PEDV outbreaks in Asia and will guide future efforts to effectively prevent and control PEDV. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  10. Epidemiological relationships of Campylobacter jejuni strains isolated from humans and chickens in South Korea.

    PubMed

    Oh, Jae-Young; Kwon, Yong-Kuk; Wei, Bai; Jang, Hyung-Kwan; Lim, Suk-Kyung; Kim, Cheon-Hyeon; Jung, Suk-Chan; Kang, Min-Su

    2017-01-01

    Thirty-nine human isolates of Campylobacter jejuni obtained from a national university hospital during 2007-2010 and 38 chicken isolates of C. jejuni were collected from poultry farms during 2009-2010 in South Korea were used in this study. Campylobacter genomic species and virulence-associated genes were identified by PCR. Pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) were performed to compare their genetic relationships. All isolates were highly resistant to ciprofloxacin, nalidixic acid, and tetracycline. Of all isolates tested, over 94% contained seven virulence associated genes (flaA, cadF, racR, dnaJ, cdtA, cdtB, and cdtC). All isolates were classified into 39 types by PFGE clustering with 90% similarity. Some chicken isolates were incorporated into some PFGE types of human isolates. MLST analysis for the 39 human isolates and 38 chicken isolates resulted in 14 and 23 sequence types (STs), respectively, of which 10 STs were new. STs overlapped in both chicken and human isolates included ST-21, ST-48, ST-50, ST-51, and ST-354, of which ST-21 was the predominant ST in both human and chicken isolates. Through combined analysis of PFGE types and STs, three chicken isolates were clonally related to the three human isolates associated with food poisoning (VII-ST-48, XXII-ST-354, and XXVIII-ST-51). They were derived from geographically same or distinct districts. Remarkably, clonal spread of food poisoning pathogens between animals and humans was confirmed by population genetic analysis. Consequently, contamination of campylobacters with quinolone resistance and potential virulence genes in poultry production and consumption may increase the risk of infections in humans.

  11. Geographical origin of Plasmodium vivax in the Republic of Korea: haplotype network analysis based on the parasite's mitochondrial genome.

    PubMed

    Iwagami, Moritoshi; Hwang, Seung-Young; Fukumoto, Megumi; Hayakawa, Toshiyuki; Tanabe, Kazuyuki; Kim, So-Hee; Kho, Weon-Gyu; Kano, Shigeyuki

    2010-06-25

    The Republic of Korea (South Korea) is one of the countries where vivax malaria had been successfully eradicated by the late 1970s. However, re-emergence of vivax malaria in South Korea was reported in 1993. Several epidemiological studies and some genetic studies using antigenic molecules of Plasmodium vivax in the country have been reported, but the evolutionary history of P. vivax has not been fully understood. In this study, the origin of the South Korean P. vivax population was estimated by molecular phylogeographic analysis. A haplotype network analysis based on P. vivax mitochondrial (mt) DNA sequences was conducted on 11 P. vivax isolates from South Korea and another 282 P. vivax isolates collected worldwide. The network analysis of P. vivax mtDNA sequences showed that the coexistence of two different groups (A and B) in South Korea. Groups A and B were identical or close to two different populations in southern China. Although the direct introduction of the two P. vivax populations in South Korea were thought to have been from North Korea, the results of this analysis suggest the genealogical origin to be the two different populations in southern China.

  12. Arenaviruses and hantaviruses: from epidemiology and genomics to antivirals.

    PubMed

    Charrel, R N; Coutard, B; Baronti, C; Canard, B; Nougairede, A; Frangeul, A; Morin, B; Jamal, S; Schmidt, C L; Hilgenfeld, R; Klempa, B; de Lamballerie, X

    2011-05-01

    The arenaviruses and hantaviruses are segmented genome RNA viruses that are hosted by rodents. Due to their association with rodents, they are globally widespread and can infect humans via direct or indirect routes of transmission, causing considerable human morbidity and mortality. Nevertheless, despite their obvious and emerging importance as pathogens, there are currently no effective antiviral drugs (except ribavirin which proved effective against Lassa virus) with which to treat humans infected by any of these viruses. The EU-funded VIZIER project (Comparative Structural Genomics of Viral Enzymes Involved in Replication) was instigated with an ultimate view of contributing to the development of antiviral therapies for RNA viruses, including the arenaviruses and bunyaviruses. This review highlights some of the major features of the arenaviruses and hantaviruses that have been investigated during recent years. After describing their classification and epidemiology, we review progress in understanding the genomics as well as the structure and function of replicative enzymes achieved under the VIZIER program and the development of new disease control strategies.

  13. Leptospira species molecular epidemiology in the genomic era.

    PubMed

    Caimi, K; Repetto, S A; Varni, V; Ruybal, P

    2017-10-01

    Leptospirosis is a zoonotic disease which global burden is increasing often related to climatic change. Hundreds of whole genome sequences from worldwide isolates of Leptospira spp. are available nowadays, together with online tools that permit to assign MLST sequence types (STs) directly from raw sequence data. In this work we have applied R7L-MLST to near 500 genomes and strains collection globally distributed. All 10 pathogenic species as well as intermediate were typed using this MLST scheme. The correlation observed between STs and serogroups in our previous work, is still satisfied with this higher dataset sustaining the implementation of MLST to assist serological classification as a complementary approach. Bayesian phylogenetic analysis of concatenated sequences from R7-MLST loci allowed us to resolve taxonomic inconsistencies but also showed that events such as recombination, gene conversion or lateral gene transfer played an important role in the evolution of Leptospira genus. Whole genome sequencing allows us to contribute with suitable epidemiologic information useful to apply in the design of control strategies and also in diagnostic methods for this illness. Copyright © 2017 Elsevier B.V. All rights reserved.

  14. The complete genomic sequence of a tentative new polerovirus identified in barley in South Korea.

    PubMed

    Zhao, Fumei; Lim, Seungmo; Yoo, Ran Hee; Igori, Davaajargal; Kim, Sang-Min; Kwak, Do Yeon; Kim, Sun Lim; Lee, Bong Choon; Moon, Jae Sun

    2016-07-01

    The complete nucleotide sequence of a new barley polerovirus, tentatively named barley virus G (BVG), which was isolated in Gimje, South Korea, has been determined using an RNA sequencing technique combined with polymerase chain reaction methods. The viral genomic RNA of BVG is 5,620 nucleotides long and contains six typical open reading frames commonly observed in other poleroviruses. Sequence comparisons revealed that BVG is most closely related to maize yellow dwarf virus-RMV, with the highest amino acid identities being less than 90 % for all of the corresponding proteins. These results suggested that BVG is a member of a new species in the genus Polerovirus.

  15. Using field-based epidemiological methods to investigate FMD outbreaks: an example from the 2002 outbreak in Korea.

    PubMed

    Wee, S-H; Nam, H-M; Moon, O-K; Yoon, H; Park, J-Y; More, S J

    2008-12-01

    Relevant to foot and mouth disease (FMD), most published epidemiological studies have been conducted using quantitative methods and substantial regional or national datasets. Veterinary epidemiology also plays a critical role during outbreak investigations, both to assist with herd-level decision-making and to contribute relevant information to assist with ongoing national or regional control strategies. Despite the importance of this role, however, little information has been published on the use of applied (field-based) epidemiological methods during disease outbreaks. In this study, we outline an investigative template for FMD, and a case study of its use during the 2002 FMD outbreak in Korea. Suitable for use during field-based epidemiological investigations of individual farms within a broader regional/national response, the template considers three steps including confirming infection, estimating date of introduction and determining method of introduction. A case study was conducted on IP13 (the 13th infected premises), the only IP during the 2002 FMD outbreak in Korea that was geographically isolated from all other known cases. The authorities first became aware of FMD on IP13 on 2 June, however, infection may have been present from 12 May. Infection was confirmed on 3 June 2002. FMD was probably spread to IP13 by a contract worker who had participated during 2-4 May in the culling operations on IP1. Other routes of spread were ruled out during the investigation. The contract worker lived in the locality of IP13 and worked on a part-time basis at a pork-processing plant that was adjacent to this farm. The contractor became heavily contaminated during the cull, but did not comply fully with cleaning and disinfection requirements once the cull had been completed. The investigative template contributed structure and focus to the field-based investigation. Results from this case study demonstrate the need for strict management of personnel in disease control and

  16. Comparative genomics of QX-like infectious bronchitis viruses in Korea.

    PubMed

    Hong, Seung-Min; Kwon, Hyuk-Joon; Choi, Kang-Seuk; Kim, Jae-Hong

    2017-05-01

    To minimize the spread of infectious bronchitis virus (IBV), domestic fowl have been extensively vaccinated with the KM91 strain. However, various IBV QX-like virus strains have become increasingly prevalent in Korea. We conducted comparative genomic analyses of seven QX-like viruses: early viruses (n = 2), new cluster 1 (NC1; recombinants of KM91 and the early QX-like viruses, n = 3) and recurrent viruses (n = 2), to understand their genomic backgrounds. The early and NC1 viruses had KM91-like backgrounds, but the recurrent viruses had QX-like genomic backgrounds. The absence of pure QX-like viruses before the appearance of the early viruses suggests that the viruses were introduced from other countries after recombination, but the NC1 viruses originated in Korea. The recent prevalence of recurrent viruses with different genomic backgrounds and spike genes from the early and the NC1 viruses may indicate the repeated introduction of different infectious bronchitis viruses from other countries and their successful evasion of vaccine immunity in the field. Furthermore, a 1ab gene-based phylogenetic analysis revealed three distinct lineages: North America-Europe, China/Taiwan, and China. KM91 and the early and NC1 viruses were included in the North America-Europe lineage, and the recurrent QX-like viruses were included in the China lineage. The phylogenetic positions of KM91-like 1ab and QX-like spike suggest frequent recombination between the North America-Europe and China lineages. Additional studies on the patterns of recombination, including donor-acceptor relationships, geographical sites, and non-poultry hosts, may be valuable for understanding the evolution of IBVs.

  17. Microreact: visualizing and sharing data for genomic epidemiology and phylogeography

    PubMed Central

    Argimón, Silvia; Abudahab, Khalil; Goater, Richard J. E.; Fedosejev, Artemij; Bhai, Jyothish; Glasner, Corinna; Feil, Edward J.; Holden, Matthew T. G.; Yeats, Corin A.; Grundmann, Hajo; Spratt, Brian G.

    2016-01-01

    Visualization is frequently used to aid our interpretation of complex datasets. Within microbial genomics, visualizing the relationships between multiple genomes as a tree provides a framework onto which associated data (geographical, temporal, phenotypic and epidemiological) are added to generate hypotheses and to explore the dynamics of the system under investigation. Selected static images are then used within publications to highlight the key findings to a wider audience. However, these images are a very inadequate way of exploring and interpreting the richness of the data. There is, therefore, a need for flexible, interactive software that presents the population genomic outputs and associated data in a user-friendly manner for a wide range of end users, from trained bioinformaticians to front-line epidemiologists and health workers. Here, we present Microreact, a web application for the easy visualization of datasets consisting of any combination of trees, geographical, temporal and associated metadata. Data files can be uploaded to Microreact directly via the web browser or by linking to their location (e.g. from Google Drive/Dropbox or via API), and an integrated visualization via trees, maps, timelines and tables provides interactive querying of the data. The visualization can be shared as a permanent web link among collaborators, or embedded within publications to enable readers to explore and download the data. Microreact can act as an end point for any tool or bioinformatic pipeline that ultimately generates a tree, and provides a simple, yet powerful, visualization method that will aid research and discovery and the open sharing of datasets. PMID:28348833

  18. Molecular epidemiology of Japanese encephalitis virus circulating in South Korea, 1983-2005

    PubMed Central

    2010-01-01

    We sequenced the envelope (E) gene of 17 strains of the Japanese encephalitis virus (JEV) isolated in South Korea in 1983-2005 and compared the sequences with those from previously reported strains. Our results show the remarkable genetic stability of the E gene sequence in Korean JEV strains. Five pairs of E gene sequences from 10 Korean strains were identical, despite geographical differences and a maximum five-year time span. Sequence comparisons with other Asian strains revealed that the Korean strains are closely related to those from China, Japan, and Vietnam. Genotype 3 strains were predominant in Korea before 1993, when genotype 1 strain K93A07 was first isolated. The two genotypes were detected simultaneously in 1994 but since then, only genotype 1 has been isolated in South Korea. Thus, the genotype change occurred according to the year of isolation rather than the geographical origin. PMID:20546562

  19. Complete genomic sequences and comparative analysis of Mamestra brassicae nucleopolyhedrovirus isolated in Korea.

    PubMed

    Choi, Jae Bang; Heo, Won Il; Shin, Tae Young; Bae, Sung Min; Kim, Woo Jin; Kim, Ju Il; Kwon, Min; Choi, Jae Young; Je, Yeon Ho; Jin, Byung Rae; Woo, Soo Dong

    2013-08-01

    Mamestra brassicae nucleopolyhedrovirus-K1 (MabrNPV-K1) was isolated from naturally infected M. brassicae (Lepidoptera: Noctuidae) larvae in Korea. The full genome sequences of MabrNPV-K1 were determined, analysed and compared to those of other baculoviruses. The MabrNPV-K1 genome consisted of 152,710 bp and had an overall G + C content of 39.9%. Computer-assisted analysis predicted 158 open reading frames (ORFs) of 150 nucleotides or greater that showed minimal overlap. Two inhibitor of apoptosis (iap) and six baculovirus repeated ORFs were interspersed in the MabrNPV-K1 genome. The unique MabrNPV-K1 ORF133 was identified in the MabrNPV-K1 genome that was not previously reported in baculoviruses. The gene content and arrangement in MabrNPV-K1 had the highest similarity with those of Helicoverpa armigera MNPV (HearMNPV) and Mamestra configurata NPV-B (MacoNPV-B), and their shared homologous genes were 99% collinear. The MabrNPV-K1 genome contained four homologous repeat regions (hr1, hr2, hr3 and hr4) that accounted for 3.3% of the genome. The genomic positions of the four MabrNPV-K1 hr regions were conserved among those of HearMNPV and MacoNPV-B. The gene parity plot, percent identity of the gene homologues and a phylogenetic analysis suggested that these three viruses are closely related not only to each other but also to the same virus strains rather than different virus species.

  20. Gene set analyses of genome-wide association studies on 49 quantitative traits measured in a single genetic epidemiology dataset.

    PubMed

    Kim, Jihye; Kwon, Ji-Sun; Kim, Sangsoo

    2013-09-01

    Gene set analysis is a powerful tool for interpreting a genome-wide association study result and is gaining popularity these days. Comparison of the gene sets obtained for a variety of traits measured from a single genetic epidemiology dataset may give insights into the biological mechanisms underlying these traits. Based on the previously published single nucleotide polymorphism (SNP) genotype data on 8,842 individuals enrolled in the Korea Association Resource project, we performed a series of systematic genome-wide association analyses for 49 quantitative traits of basic epidemiological, anthropometric, or blood chemistry parameters. Each analysis result was subjected to subsequent gene set analyses based on Gene Ontology (GO) terms using gene set analysis software, GSA-SNP, identifying a set of GO terms significantly associated to each trait (pcorr < 0.05). Pairwise comparison of the traits in terms of the semantic similarity in their GO sets revealed surprising cases where phenotypically uncorrelated traits showed high similarity in terms of biological pathways. For example, the pH level was related to 7 other traits that showed low phenotypic correlations with it. A literature survey implies that these traits may be regulated partly by common pathways that involve neuronal or nerve systems.

  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. Epidemiological features and surveillance performance of measles in the Republic of Korea, 2002-2011.

    PubMed

    Choe, Young June; Park, Young-Joon; Eom, Hye Suk; Kim, Eun Seong; Bae, Geun-Ryang; Lee, Jong-Koo

    2013-01-01

    Measles was declared eliminated from the Republic of Korea in 2006; however, recently the number of reported cases has been gradually increasing. To address this issue, we summarized the measles surveillance data collected during 2002-2011, and aimed to evaluate the performance of the current surveillance system in Korea. We analyzed data from the national surveillance system to describe the occurrence of measles. Surveillance indicators proposed by the World Health Organization were used to evaluate the performance of the current measles surveillance system. Between 2002 and 2005, a gradual decrease in confirmed cases of measles was noted, whereas cyclical increases were noted from 2006 to 2011. Since 2006, confirmed cases of measles were more likely to be identified by laboratory methods. In general, the incidence of confirmed case was less than one per million in Korea; however, this figure increased in 2002 (1.3/million), 2007 (4.0), and 2010 (2.3). Most cases were occurred in the age groups 0-23 months and 12-17 years. Laboratory testing was performed in most suspected cases; however, the proportion of discarded cases was low. Overall, more than half of the reported cases experienced an onset of symptoms from April to June. The incidence of measles is relatively low in Korea, and the laboratory surveillance may have helped in identifying under-diagnosed cases within the country. It remains important to continuously assess the surveillance data to improve the surveillance performance.

  3. 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

  4. RETROSPECTIVE ANALYSIS OF THE EPIDEMIOLOGIC LITERATURE, 1990-2015, ON WILDLIFE-ASSOCIATED DISEASES FROM THE REPUBLIC OF KOREA.

    PubMed

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

    2017-01-01

    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 Korea Ministry of Health and Welfare or the Korea Ministry of Agriculture, Food and Rural Affairs. Two diseases were reported as occurring as epidemics; highly pathogenic avian influenza (HPAI) and virulent Newcastle disease. Six diseases or disease agents were described in the literature as emerging including HPAI, rabies, Babesia microti , avian coronaviruses, scrub typhus, and severe fever thrombocytopenia syndrome virus. The diseases for which there were the largest number of publications were HPAI and rabies. The majority of wildlife-associated zoonotic disease publications focused on food-borne parasitic infections or rodent-associated diseases. Several publications focused on the potential of wildlife as reservoirs of livestock diseases; in particular, Korean water deer ( Hydropotes inermis argyropus ) and wild boar ( Sus scrofa ). In contrast, there were few publications on diseases of concern for wildlife populations or research to understand the impacts of these diseases for wildlife management. Increased focus on prospective studies would enhance understanding of disease dynamics in wildlife populations. For the high-consequence diseases that impact multiple sectors, a One Health approach, with coordination among the public health, agricultural

  5. Epidemiologic Study on Kawasaki Disease in Korea, 2007-2014: Based on Health Insurance Review & Assessment Service Claims.

    PubMed

    Ha, Sangmi; Seo, Gi Hyeon; Kim, Kyu Yeun; Kim, Dong Soo

    2016-09-01

    The aim of this study is to assess the actual epidemiologic features of Kawasaki disease (KD) in Korea using the data from Health Insurance Review & Assessment Service (HIRA) claims from 2007 to 2014. We investigated HIRA claims of patients who had KD (International Classification of Diseases-10, M30.3) as a major diagnosis and were given intravenous immunoglobulin (IVIG) from 2007 to 2014. A total of 39,082 patients were reported during the period. The male-to-female ratio was 1.42 and the median age was 28 months. The incidence rates were 168.3 per 100,000 population aged 0 to 4 years in 2007, 159.1 in 2008, 167.3 in 2009, 190.4 in 2010, 188.2 in 2011, 190.2 in 2012, 210.4 in 2013 and 217.2 in 2014. These rates were much higher than those in the previous studies in Korea. KD occurred more often in early summer (May, June and July) and winter (December and January). The annual incidence rate of KD had been increasing every year, reaching 217.2 per 100,000 population aged 0 to 4 years in 2014. It is the second highest incidence rate of KD in the world after Japan.

  6. Characteristics of methicillin resistant Staphylococcus aureus isolated from chicken meat and hospitalized dogs in Korea and their epidemiological relatedness.

    PubMed

    Kwon, Nam Hoon; Park, Kun Taek; Jung, Woo Kyung; Youn, Hwa Young; Lee, Yeonhee; Kim, So Hyun; Bae, Wonki; Lim, Ji Youn; Kim, Ji Yeon; Kim, Jun Man; Hong, Soon Keun; Park, Yong Ho

    2006-10-31

    Methicillin resistant Staphylococcus aureus (MRSA) is one of the most important pathogens in human and veterinary hospitals. The isolation of MRSA from animals and foodstuffs has been reported with an increased incidence. However, methicillin (oxacillin) is not used in animal husbandry or in animal hospitals in Korea. In this study, three pre-MRSA and one silent mecA-carrying methicillin susceptible S. aureus (smMSSA) were isolated from retail chicken meat, and three MRSA were isolated from hospitalized dogs in Korea. The three pre-MRSA isolates were determined to have a staphylococcal cassette chromosome mec (SCCmec) type III, and the smMSSA isolate was not classified. The animal hospital isolates were found to contain SCCmec type II. Seven and 15 S. aureus isolated from hospitalized humans and bovine milk, respectively, were also examined in this study in order to determine the epidemiological origins of MRSA. Multilocus sequencing typing (MLST) revealed that the chicken meat and bovine milk isolates were closely related to the animal hospital isolates. The SCCmec characteristics and MLST analyses indicated the possibility of the human to animal transmission of MRSA. These results highlight the importance of identifying MRSA carriers as well as intercepting MRSA transmission because MRSA is becoming increasingly widespread without any plausible relationship with the use of methicillin (oxacillin).

  7. Complete Genome Sequence of Classical Swine Fever Virus Isolated near the Demilitarized Zone in the Republic of Korea

    PubMed Central

    Song, Sok; Choe, SeEun; Cha, RaMi; Kim, Ki-Sun; Cho, In-Soo

    2017-01-01

    ABSTRACT The YC16CS (genotype 2.1) strain of classical swine fever virus, isolated from infected pigs in Yeoncheon province, Republic of Korea, near the demilitarized zone, has a high identity with the PC11WB strain of the virus. This is significant in that it is the first case of transmission from wild boars to breed pigs revealed by an epidemiological investigation. PMID:28385854

  8. Complete Genome Sequence of Classical Swine Fever Virus Isolated near the Demilitarized Zone in the Republic of Korea.

    PubMed

    Song, Sok; Choe, SeEun; Cha, RaMi; Kim, Ki-Sun; Cho, In-Soo; An, Dong-Jun

    2017-04-06

    The YC16CS (genotype 2.1) strain of classical swine fever virus, isolated from infected pigs in Yeoncheon province, Republic of Korea, near the demilitarized zone, has a high identity with the PC11WB strain of the virus. This is significant in that it is the first case of transmission from wild boars to breed pigs revealed by an epidemiological investigation. Copyright © 2017 Song et al.

  9. The role of epidemiology in the era of molecular epidemiology and genomics: Summary of the 2013 AJE-sponsored Society of Epidemiologic Research Symposium.

    PubMed

    Kuller, Lewis H; Bracken, Michael B; Ogino, Shuji; Prentice, Ross L; Tracy, Russell P

    2013-11-01

    On June 20, 2013, the American Journal of Epidemiology sponsored a symposium at the Society for Epidemiologic Research's 46th Annual Meeting in Boston, Massachusetts, entitled, "What Is the Role of Epidemiology in the Era of Molecular Biology and Genomics?" The future of epidemiology depends on innovation in generating interesting and important testable hypotheses that are relevant to population health. These new strategies will depend on new technology, both in measurement of agents and environment and in the fields of pathophysiology and outcomes, such as cellular epidemiology and molecular pathology. The populations to be studied, sample sizes, and study designs should be selected based on the hypotheses to be tested and include case-control, cohort, and clinical trials. Developing large mega cohorts without attention to specific hypotheses is inefficient, will fail to address many associations with high-quality data, and may well produce spurious results.

  10. 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.

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

    PubMed Central

    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. PMID:26770040

  12. Complete genome sequence of a novel porcine parainfluenza virus 5 isolate in Korea.

    PubMed

    Lee, Yu Na; Lee, Changhee

    2013-08-01

    A novel cytopathogenic paramyxovirus was isolated from a lung sample from a piglet, using continuous porcine alveolar macrophage cells. Morphologic and genetic studies indicated that this porcine virus (pPIV5) belongs to the species Parainfluenza 5 in the family Paramyxoviridae. We attempted to determine the complete nucleotide sequence of the first Korean pPIV5 isolate, designated KNU-11. The full-length genome of KNU-11 was found to be 15,246 nucleotides in length and consist of seven nonoverlapping genes (3'-N-V/P-M-F-SH-HN-L-5') predicted to encode eight proteins. The overall degree of nucleotide sequence identity was 98.7 % between KNU-11 and PIV5 (formerly simian virus 5, SV5), a prototype paramyxovirus, and the putative proteins had 74.4 to 99.2 % amino acid identity to those of PIV5. Phylogenetic analysis further demonstrated that the novel pPIV5 isolate is a member of the genus Rubulavirus of the subfamily Paramyxovirinae. The present study describes the identification and genomic characterization of a pPIV5 isolate in South Korea.

  13. Epidemiological studies of esophageal cancer in the era of genome-wide association studies

    PubMed Central

    Wang, An-Hui; Liu, Yuan; Wang, Bo; He, Yi-Xuan; Fang, Ye-Xian; Yan, Yong-Ping

    2014-01-01

    Esophageal cancer (EC) caused about 395000 deaths in 2010. China has the most cases of EC and EC is the fourth leading cause of cancer death in China. Esophageal squamous cell carcinoma (ESCC) is the predominant histologic type (90%-95%), while the incidence of esophageal adenocarcinoma (EAC) remains extremely low in China. Traditional epidemiological studies have revealed that environmental carcinogens are risk factors for EC. Molecular epidemiological studies revealed that susceptibility to EC is influenced by both environmental and genetic risk factors. Of all the risk factors for EC, some are associated with the risk of ESCC and others with the risk of EAC. However, the details and mechanisms of risk factors involved in the process for EC are unclear. The advanced methods and techniques used in human genome studies bring a great opportunity for researchers to explore and identify the details of those risk factors or susceptibility genes involved in the process of EC. Human genome epidemiology is a new branch of epidemiology, which leads the epidemiology study from the molecular epidemiology era to the era of genome wide association studies (GWAS). Here we review the epidemiological studies of EC (especially ESCC) in the era of GWAS, and provide an overview of the general risk factors and those genomic variants (genes, SNPs, miRNAs, proteins) involved in the process of ESCC. PMID:25133033

  14. The epidemiology of psychiatric disorders among women with breast cancer in South Korea: analysis of national registry data.

    PubMed

    Kang, Jee In; Sung, Na Young; Park, Sang Jin; Lee, Chong Gul; Lee, Byung Ook

    2014-01-01

    Population-based data on the epidemiology of psychiatric disorders in patients with breast cancer are lacking. Because the National Health Insurance (NHI) Program in South Korea is a compulsory social insurance system covering the entire Korean population, the NHI is a good source of information for epidemiological studies. In the present study, we examined the incidence of psychiatric disorders among Korean women newly diagnosed with breast cancer using the NHI Corporation (NHIC) database. Data were collected for adult women newly diagnosed with breast cancer using the claim database and cancer registration files of the NHIC from 2005 to 2008. We analysed data for women diagnosed with psychiatric disorders over a 5-year period, from 2004 (at least 1 year before the cancer registration date) to 2009 (at least 1 year after the cancer registration date). We identified 6536 patients with psychiatric disorders among 42 190 women with breast cancer. The most prevalent psychiatric disorder was anxiety disorder (N = 2518). The incidence rates of anxiety disorders, depressive disorders, sleep disorders and adjustment disorders were 27.08, 22.41, 10.57 and 4.35 cases per 1000 person-year, respectively. The incidence rates of psychiatric disorders in Korean women with breast cancer from the nationwide database were much lower than found by previous reports using screening tools. The finding implicates that psychiatric disorders among breast cancer patients tend to be underdiagnosed and undertreated in actual clinical practice. Our epidemiological findings provide important information for establishing a national strategy of cancer care to detect and manage psychiatric problems. Copyright © 2013 John Wiley & Sons, Ltd.

  15. Modeling population health: reflections on the performativity of epidemiological techniques in the age of genomics.

    PubMed

    Bauer, Susanne

    2013-12-01

    Risk reasoning has become the common-sense mode of knowledge production in the health sciences. Risk assessment techniques of modern epidemiology also co-shape the ways genomic data are translated into population health. Risk computations (e.g., in preventive medicine, clinical decision-support software, or web-based self-tests), loop results from epidemiological studies back into everyday life. Drawing from observations at various European research sites, I analyze how epidemiological techniques mediate and enact the linkages between genomics and public health. This article examines the epidemiological apparatus as a generative machine that is socially performative. The study design and its reshuffling of data and categories in risk modeling recombine old and new categories from census to genomics and realign genes/environment and nature/culture in novel and hybrid ways. In the Euro-American assemblage of risk reasoning and related profiling techniques, the individual and the population are no longer separate but intimately entangled.

  16. Epidemiology of canine distemper virus in wild raccoon dogs (Nyctereutes procyonoides) from South Korea.

    PubMed

    Cha, Se-Yeoun; Kim, Eun-Ju; Kang, Min; Jang, Sang-Ho; Lee, Hae-Beom; Jang, Hyung-Kwan

    2012-09-01

    Raccoon dogs (Nyctereutes procyonoides) are widespread and common in South Korea. In 2011, we obtained serum samples from 102 wild raccoon dogs to survey their exposure to canine distemper virus (CDV). Forty-five of the 102 animals (44.1%) were seropositive. Field cases of canine distemper in wild raccoon dogs from 2010 to 2011 were investigated. Fourteen cases of CDV infection were identified by a commercially available CDV antigen detection kit. These cases were used for virus isolation and molecular analysis. Sequence analysis of hemagglutinin genes indicated that all viruses isolated belonged to the Asia-2 genotype. H protein residues which are related to the receptor and host specificity (residues 530 and 549) were analyzed. A glutamic acid (E) residue is present at 530 in all isolates. At 549, a histidine (H) residue was found in five isolates and tyrosine (Y) residue was found in 6 isolates. Our study demonstrated that CDV infection was widespread in wild raccoon dogs in South Korea.

  17. A brief primer on genomic epidemiology: lessons learned from Mycobacterium tuberculosis.

    PubMed

    Guthrie, Jennifer L; Gardy, Jennifer L

    2017-01-01

    Genomics is now firmly established as a technique for the investigation and reconstruction of communicable disease outbreaks, with many genomic epidemiology studies focusing on revealing transmission routes of Mycobacterium tuberculosis. In this primer, we introduce the basic techniques underlying transmission inference from genomic data, using illustrative examples from M. tuberculosis and other pathogens routinely sequenced by public health agencies. We describe the laboratory and epidemiological scenarios under which genomics may or may not be used, provide an introduction to sequencing technologies and bioinformatics approaches to identifying transmission-informative variation and resistance-associated mutations, and discuss how variation must be considered in the light of available clinical and epidemiological information to infer transmission. © 2016 New York Academy of Sciences.

  18. 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

  19. 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

  20. Epidemiology of Campylobacter jejuni outbreak in a middle school in Incheon, Korea.

    PubMed

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

    2010-11-01

    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.

  1. A reference pan-genome approach to comparative bacterial genomics: identification of novel epidemiological markers in pathogenic Campylobacter.

    PubMed

    Méric, Guillaume; Yahara, Koji; Mageiros, Leonardos; Pascoe, Ben; Maiden, Martin C J; Jolley, Keith A; Sheppard, Samuel K

    2014-01-01

    The increasing availability of hundreds of whole bacterial genomes provides opportunities for enhanced understanding of the genes and alleles responsible for clinically important phenotypes and how they evolved. However, it is a significant challenge to develop easy-to-use and scalable methods for characterizing these large and complex data and relating it to disease epidemiology. Existing approaches typically focus on either homologous sequence variation in genes that are shared by all isolates, or non-homologous sequence variation--focusing on genes that are differentially present in the population. Here we present a comparative genomics approach that simultaneously approximates core and accessory genome variation in pathogen populations and apply it to pathogenic species in the genus Campylobacter. A total of 7 published Campylobacter jejuni and Campylobacter coli genomes were selected to represent diversity across these species, and a list of all loci that were present at least once was compiled. After filtering duplicates a 7-isolate reference pan-genome, of 3,933 loci, was defined. A core genome of 1,035 genes was ubiquitous in the sample accounting for 59% of the genes in each isolate (average genome size of 1.68 Mb). The accessory genome contained 2,792 genes. A Campylobacter population sample of 192 genomes was screened for the presence of reference pan-genome loci with gene presence defined as a BLAST match of ≥ 70% identity over ≥ 50% of the locus length--aligned using MUSCLE on a gene-by-gene basis. A total of 21 genes were present only in C. coli and 27 only in C. jejuni, providing information about functional differences associated with species and novel epidemiological markers for population genomic analyses. Homologs of these genes were found in several of the genomes used to define the pan-genome and, therefore, would not have been identified using a single reference strain approach.

  2. Analysis of the nonstructural and structural polyprotein regions, and complete genome sequences of Israel acute paralysis viruses identified from honeybees (Apis mellifera) in Korea.

    PubMed

    Reddy, Kondreddy Eswar; Noh, Jin Hyeong; Kim, Young-Ha; Yoo, Mi Sun; Doan, Huong Thi Thanh; Ramya, Mummadireddy; Jung, Suk-Chan; Quyen, Dong Van; Kang, Seung-Won

    2013-09-01

    Phylogenetic trees were constructed for 24 partial nucleotide sequences of the nonstructural polyprotein (ORF1) and structural polyprotein regions (ORF2) of Korean IAPV genotypes, as well as eight previously reported IAPV sequences from various countries. Most of the Korean genotypes formed a distinct cluster, separate from other country genotypes. To investigate this phenomenon in more detail, three complete IAPV genome sequences were identified from different regions in Korea, i.e., Korea1, Korea2, and Korea3. These sequences were aligned with eight previously reported complete genome sequences and various genome regions were compared. The Korean IAPVs were very similar to those from China and Israel, but highly diverged from USA and Australian genotypes. Interestingly, they showed greater variability than the USA and Australian genotypes in ORF1, but highly similar to the Australian genotype in the ORF2 region. Thus, genetic recombination may account for the spatial distance between the Korean IAPV genotypes and those from other countries.

  3. Trends of Antibiotic Consumption in Korea According to National Reimbursement Data (2008-2012): A Population-Based Epidemiologic Study.

    PubMed

    Yoon, Young Kyung; Park, Gi Chan; An, Hyonggin; Chun, Byung Chul; Sohn, Jang Wook; Kim, Min Ja

    2015-11-01

    This study determined the trends in the quantities and patterns of nationwide antibiotic consumption in the Republic of Korea (ROK).This nationwide descriptive epidemiological study was conducted in the ROK between 2008 and 2012. The quantities and patterns of total systemic antibiotic prescriptions were analyzed using National Health Insurance claims data collected through the Health Insurance Review and Assessment service. Data concerning systemic antibiotics were collected using measurement units of the defined daily dose (DDD) per 1000 people per day according to the Anatomical Therapeutic Chemical classification.Over the 5-year study period, the annual consumption of systemic antibiotics ranged from 21.68 to 23.12 DDD per 1000 people per day. Outpatient antibiotic use accounted for 80.9% of total consumption. A regression model with autoregressive errors showed significant increased consumption of major antibiotic subgroups, including 3rd-generation cephalosporins, carbapenems, and glycopeptides (P < 0.001). However, the antibiotic use of 1st- (P = 0.003), 2nd- (P = 0.004), and 3rd-generation (P = 0.018) cephalosporins among patients who underwent surgery under monitoring by the antimicrobial stewardship programs for perioperative prescription was significantly lower than in those who underwent surgery without monitoring programs. In time-series analysis, total antibiotic consumption demonstrated significant seasonality (P < 0.001).The consumption of broad-spectrum antibiotics was noted to have increased in the ROK from 2008 to 2012, providing a possible explanation for the changing epidemiology of multidrug resistance. Larger prospective studies are needed to investigate the impact on public health of monitoring programs of perioperative antibiotic usage.

  4. [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.

  5. The Center for Epidemiological Studies Depression Scale in older community samples in Indonesia, North Korea, Myanmar, Sri Lanka, and Thailand.

    PubMed

    Mackinnon, A; McCallum, J; Andrews, G; Anderson, I

    1998-11-01

    Cultural differences in the reporting of depressive symptoms among older people were examined using the Center for Epidemiological Studies Depression (CES-D) scale in five Southeast Asian countries: Indonesia, Korea, Myanmar, Sri Lanka, and Thailand. Previous work in Asian samples--principally North American immigrants--suggested differential functioning of the CES-D. The four-factor solution established in the original studies of the CES-D was replicated for all countries using a confirmatory factor analytic approach. It was, however, demonstrated that little information was lost in considering full-scale scores rather than the four subscales separately. The behavior of the CES-D in older Asian populations was found to be comparable to results obtained in North American and European cultures. Significant somatization of depression in these Asian samples was not found. There appears to be a general factor measuring depressed mood across older populations. The results support the validity of comparing responses on the CES-D across cultures.

  6. 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.

  7. Molecular epidemiological investigation of foot-and-mouth disease virus in Korea in 2000.

    PubMed

    Shin, Jin-Ho; Sohn, Hyun-Joo; Choi, Kang-Seuk; Kwon, Byung-Jun; Ko, Young-Joon; An, Dong-Jun; Cha, Sang-Ho; Park, Jong-Hyeon; Jeong, Woo-Seog; Park, Jee-Yong; Choi, Cheong-Up; Kweon, Chang-Hee; Song, Jae-Young; Kim, Jong-Yeom; An, Soo-Hwan; Kim, Soon-Jae; Joo, Yi-Seok

    2003-01-01

    The genetic relatedness of 7 Korean type O field strains of foot-and-mouth disease virus (FMDV) in clinical specimens collected from 5 different geographic locations in 2000 was investigated. The sequence of 162 nucleotides (nt 478-639) at the 3' end of the 1D (VP1) genes was determined from amplified cDNA fragments, and subjected to the analysis for the sequence identity/divergence and phylogenetic relationship. The overall nucleotide sequence divergence among the 7 field strains was 0 to 3.8%, suggesting that they are closely related to each other. Phylogenetic analysis with the known Middle East-South Asia (ME-SA) topotype strains showed that the 7 Korean field strains formed two distinct clusters within the same lineage of the ME-SA topotype strains. Cluster 1 consisted of the strains of the primary foci of infection (Paju and Hongseong), and closely related to the strains prevailed in the Far East. Cluster 2 comprised those of subsequently affected regions (Boryeong, Yongin, and Chungju), and was further diverged from the Cluster 1. The result of phylogenetic analysis indicated that the Korean strains may have evolved from a common ancestor of the Pan Asia strains, and that at least 2 phylogenetically clustered variants within the same lineage were prevalent during the epidemic. The potential origin and sources of the virus introduction to Korea were discussed.

  8. Epidemiological evidence in law: a comment on Supreme Court Decision 2011Da22092, South Korea.

    PubMed

    Broadbent, Alex

    2015-01-01

    This paper offers a commentary on three aspects of the Supreme Court's recent decision (2011Da22092). First, contrary to the Court's finding, this paper argues that epidemiological evidence can be used to estimate the probability that a given risk factor caused a disease in an individual plaintiff. Second, the distinction between specific and non-specific diseases, upon which the Court relies, is shown to be without scientific basis. Third, this commentary points out that the Court's finding concerning defect of expression effectively enables tobacco companies to profit from the efforts of epidemiologists and others involved in public health to raise awareness of the dangers of smoking.

  9. 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. © 2013 Blackwell Verlag GmbH.

  10. 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

  11. Real world epidemiology of myeloproliferative neoplasms: a population based study in Korea 2004-2013.

    PubMed

    Byun, Ja Min; Kim, Young Jin; Youk, Taemi; Yang, John Jeongseok; Yoo, Jongha; Park, Tae Sung

    2017-03-01

    Myeloproliferative neoplasms (MPNs), with an expected increment in number, impose substantial economic and social burdens. To this end, we conducted a nationwide population-based descriptive epidemiology study. We also investigated medical cost associated with MPNs. Prevalence was the highest for essential thrombocythemia (ET) (range 4.1-9.0 per 100,000), followed by polycythemia vera (PV) (range 2.8-5.4 per 100,000) and primary myelofibrosis (PMF) (range 0.5-0.9 per 100,000). ET incurred the highest cumulative total cost at US$35 million and the most frequent hospital visits, while PMF incurred the highest average cost per person at US$5000. The mean hemoglobin level was 16.9 ± 2.2 g/dL for PV males and 15.5 ± 2.7 g/dL for PV females. Further analyses on hemoglobin levels showed the true positive rate of PV from the significantly elevated hemoglobin group (defined as >18.5 g/dL for men and >16.5 g/dL for women) was 3.01% and that of MPNs was 3.1%. Here, we provide the biggest population-based report on MPN epidemiology that can readily be used as a representative Asian data.

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

    PubMed

    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

    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 ((137)Cs) in Seoul. Using information regarding the frequency and duration of passing via the (137)Cs 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. 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. An individual exposure assessment was performed for an epidemiological study to estimate the health risk among residents living in the vicinity of (137)Cs contaminated roads. The average exposure dose in the exposed people was less than 5% of the current guideline.

  13. Epidemiological trends and risk factors in major burns patients in South Korea: a 10-year experience.

    PubMed

    Seo, Dong Kook; Kym, Dohern; Yim, Haejun; Yang, Hyeong Tae; Cho, Yong Suk; Kim, Jong Hyun; Hur, Jun; Chun, Wook

    2015-02-01

    To determine epidemiological trends among burns patients admitted to our burns center during 2003-2012, and the usefulness of the Abbreviated Burns Severity Index (ABSI) for predicting burns-related mortality. We retrospectively reviewed the data of 4481 burns patients. We analyzed the epidemiological trends and ABSI scores using Student t-test and one-way analysis of variance (continuous variables), chi-square test (categorical variables) and stepwise logistic-regression analysis (predictors of mortality). The mean age and male-to-female ratio were 39.9±19.7 years and 2.88, respectively. ABSI scores decreased from 7.7±3.0 in 2003 to 6.9±3.0 in 2012. Mortality rate improved from 24.5% in 2003 to 15.8% in 2012. Burns were caused by flames (67.3%), scalding (22.0%) and electrical (7.5%), chemical (1.6%) and contact (1.5%) injuries. Scalding and flames were the most common causes in patients aged ≤20 years and ≥21 years, respectively. Female sex, inhalation injury, full-thickness burns, large total body surface area (TBSA) burned and old age predicted mortality. ABSI scores <4 and >14 were associated with 0.7% and >90% mortality, respectively. The mortality of major burns has decreased but remains high. ABSI scores predict burns-related mortality. Copyright © 2014 Elsevier Ltd and ISBI. All rights reserved.

  14. 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

  15. Declaring a tuberculosis outbreak over with genomic epidemiology.

    PubMed

    Hatherell, Hollie-Ann; Didelot, Xavier; Pollock, Sue L; Tang, Patrick; Crisan, Anamaria; Johnston, James C; Colijn, Caroline; Gardy, Jennifer L

    2016-05-01

    We report an updated method for inferring the time at which an infectious disease was transmitted between persons from a time-labelled pathogen genome phylogeny. We applied the method to 48 Mycobacterium tuberculosis genomes as part of a real-time public health outbreak investigation, demonstrating that although active tuberculosis (TB) cases were diagnosed through 2013, no transmission events took place beyond mid-2012. Subsequent cases were the result of progression from latent TB infection to active disease, and not recent transmission. This evolutionary genomic approach was used to declare the outbreak over in January 2015.

  16. Declaring a tuberculosis outbreak over with genomic epidemiology

    PubMed Central

    Hatherell, Hollie-Ann; Didelot, Xavier; Pollock, Sue L.; Tang, Patrick; Crisan, Anamaria; Johnston, James C.; Colijn, Caroline

    2016-01-01

    We report an updated method for inferring the time at which an infectious disease was transmitted between persons from a time-labelled pathogen genome phylogeny. We applied the method to 48 Mycobacterium tuberculosis genomes as part of a real-time public health outbreak investigation, demonstrating that although active tuberculosis (TB) cases were diagnosed through 2013, no transmission events took place beyond mid-2012. Subsequent cases were the result of progression from latent TB infection to active disease, and not recent transmission. This evolutionary genomic approach was used to declare the outbreak over in January 2015. PMID:28348853

  17. Epidemiological evidence in law: a comment on Supreme Court Decision 2011Da22092, South Korea

    PubMed Central

    Broadbent, Alex

    2015-01-01

    This paper offers a commentary on three aspects of the Supreme Court’s recent decision (2011Da22092). First, contrary to the Court’s finding, this paper argues that epidemiological evidence can be used to estimate the probability that a given risk factor caused a disease in an individual plaintiff. Second, the distinction between specific and non-specific diseases, upon which the Court relies, is shown to be without scientific basis. Third, this commentary points out that the Court’s finding concerning defect of expression effectively enables tobacco companies to profit from the efforts of epidemiologists and others involved in public health to raise awareness of the dangers of smoking. PMID:26063352

  18. Use of the Center for Epidemiologic Studies Depression (CES-D) Scale in Korea.

    PubMed

    Cho, M J; Kim, K H

    1998-05-01

    We translated the Center for Epidemiologic Studies Depression (CES-D) Scale into Korean, paying careful attention to culturally different modes of expression of depressive feelings and thoughts. The final translated version (CES-D-K) was administered to 164 psychiatric patients and 464 normal subjects residing in the community. Reliability, validity, and the optimal cutoff point of this scale were estimated, including ROC analysis. The CES-D-K was reliable and valid for the Korean population. Two optimal cutoff points were suggested: 24/25, the point which best corresponded to the clinical diagnosis of depression, and 20/21, which most effectively detects and covers depressive symptoms during screening. The higher cutoff points than those in Western countries may be due to different ways of expression affect, especially the suppression of positive affect, in cultures based on Confucian ethics.

  19. 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.

  20. Epidemiological Characterization of Opportunistic Mycoses between the Years 2006 and 2010 in Korea.

    PubMed

    Park, Je-Seop; Cho, Seung-Hak; Youn, Seung-Ki; Bak, Young-Seok; Yu, Young-Bin; Kim, Young Kwon

    2016-01-01

    In order to perform an epidemiological characterization of opportunistic mycosis infections, we collected health insurance data between the years 2006 and 2010 from the Health Insurance Corporation and analyzed the data to determine the prevalence of opportunistic mycoses and treatment management of opportunistic mycoses. The prevalence within the study increased consecutively by 0.02% to 0.12% every year. The annual prevalence of opportunistic mycoses increased from 2.437% in 2006 to 2.709% in 2010. The average annual prevalence was 2.605%. Candidiasis occurred the most frequently, followed by aspergillosis, zygomycosis, and cryptococcosis. The regions with the highest incidences were the capital areas, Gyeonggi and Seoul. By sex, the prevalence in females (4.851%) was 14 times higher than that in males (0.352%). Interestingly, the adults from the 20- to 49-year-old age group showed higher prevalence than children and the elderly. The average duration of hospitalized treatment was 17.31 days and of outpatient treatment was 2.21 days; 3,577 hundred million won was used in total for medical expenses. This study provides useful data to study trends of opportunistic mycoses.

  1. [Preventive medicine in times of a rapid epidemiologic transition in Korea].

    PubMed

    Park, Jung Han

    2006-01-01

    Ever since the foundation of the Korean Society for Preventive Medicine in 1947, members of the Society had made remarkable contributions to the public health development and national health promotion. They had played key roles in establishing national health system, improving environmental hygiene, controlling infectious and chronic diseases, promoting family planning, improving industrial and environmental health, and developing health service management. However, the Society had less actively responded to the changes in health service needs of the population that were caused by a rapid epidemiologic transition in last a few decades. Early detection and treatment of chronic diseases including cancer and cardiovascular diseases and risk reduction by the life style modification are major approaches to the contemporary national health problems and they are the core contents of preventive medicine. The author proposed to develop the clinical preventive medicine specialist who will have additional training in clinical medicine for health screening and life style modification to the current preventive medicine training program and thus will be able to provide comprehensive preventive medical services. Another area that the Society may take the initiative is training preventive medicine specialist in the disaster, including bioterrorism, preparedness and management. The Society should be more active in proposing health policy and health service program and also participate collectively in a large scale health research project of the government. These approaches may not only contribute more effectively to the national health promotion but also improve the identity of the Society.

  2. Whole-Genome Sequencing Elucidates Epidemiology of Nosocomial Clusters of Acinetobacter baumannii

    PubMed Central

    Willems, Stefanie; Kampmeier, Stefanie; Bletz, Stefan; Kossow, Annelene; Köck, Robin; Kipp, Frank

    2016-01-01

    We characterized two epidemiologically similar Acinetobacter baumannii clusters from two separate intensive care units (ICU) using core genome multilocus sequence typing. Clonal spread was confirmed in ICU-1 (12 of 14 isolates shared genotypes); in ICU-2, all genotypes (13 isolates) were diverse, thus excluding transmissions and enabling adequate infection control measures. PMID:27358465

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

    USDA-ARS?s Scientific Manuscript database

    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 ...

  4. 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

    2017-01-01

    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

  5. Clinical and molecular epidemiological features of hemorrhagic fever with renal syndrome in Korea over a 10-year period.

    PubMed

    Noh, Ji Yun; Cheong, Hee Jin; Song, Joon Young; Kim, Woo Joo; Song, Ki-Joon; Klein, Terry A; Lee, Sam H; Yanagihara, Richard; Song, Jin-Won

    2013-09-01

    Laboratory diagnosis of hemorrhagic fever with renal syndrome (HFRS), an infectious disease caused by rodent-borne hantaviruses in Asia and Europe, depends primarily on serological methods. Since the advent of such serodiagnostic tests, few reports are available about the clinical and molecular epidemiological features of HFRS. To investigate the epidemioclinical features of HFRS patients treated at a tertiary-care teaching hospital in Seoul over a 10-year period. Medical records of HFRS patients, admitted to a tertiary-care teaching hospital during February 2002 to February 2012, were reviewed. Sera from patients were tested for Hantaan virus (HTNV) and Seoul virus (SEOV) RNA using RT-PCR. Among 35 HFRS patients (mean age was 44.2±14.7 years), 29 were male (82.9%). Acute renal failure developed in 27 patients (77.1%), and 12 patients (34.3%) were admitted to the intensive care unit (ICU). Conjunctival injection (OR 10.32, 95% CI 1.09-97.77, P=.04) and initial serum albumin less than 3g/dL (OR 22.83, 95% CI 1.45-359.93, P=.03) were risk factors for ICU admission. Of 35 acute-phase sera, 11 (31.4%) were positive for HTNV RNA. None were positive for SEOV RNA. HFRS was characterized by the clinical triad of fever, renal insufficiency and gastrointestinal symptoms. Conjunctival injection and serum albumin level were related to severity. A large-scale multi-center study is needed to enhance insights into epidemioclinical characteristics of HFRS in Korea. Copyright © 2013 Elsevier B.V. All rights reserved.

  6. Characteristics of the Molecular Epidemiology of CTX-M-Producing Escherichia coli Isolated from a Tertiary Hospital in Daejeon, Korea.

    PubMed

    Kim, Semi; Sung, Ji Youn; Cho, Hye Hyun; Kwon, Kye Chul; Koo, Sun Hoe

    2016-09-28

    The aims of this study were to characterize the molecular epidemiological profiles of CTX-M-producing uropathogenic Escherichia coli isolates from a tertiary hospital in Daejeon, Korea, and to investigate the genetic diversity and compare the prevalence of sequence types (STs) in different areas. Extended spectrum β-lactamase-producing E. coli strains isolated from urine were analyzed for CTX-M, integrons, and insertion sequence common regions (ISCRs) by PCR and sequencing. Multilocus sequence typing (MLST), pulsed-field gel electrophoresis (PFGE), phylogenetic analysis, and rep-PCR were also used for molecular typing of the isolates. Of 80 CTX-M producers, 31 and 46 expressed CTX-M-15 and CTX-M-14, respectively. MLST analysis indicated that the most prevalent ST was ST131 (n = 34, 42.5%), followed by ST38 (n = 22, 27.5%), ST405 (n = 8, 10.0%), and ST69 (n = 6, 7.5%). Most CTX-M producers harbored class 1 integrons. ST131 strains belonged to phylogenetic group B2 and showed identical rep-PCR patterns, whereas ST69, ST38, and ST405 strains belonged to phylogenetic group D; the ST38 and ST405 strains displayed the same rep-PCR pattern, respectively. ST131 and ST38 isolates showed 21 and 19 distinct types, respectively, by PFGE. In Daejeon, D-ST38 CTX-M-14 producers were relatively more prevalent than in other countries and Korean cities. Our results indicate that CTX-M-producing E. coli isolates belonged mostly to ST131 or ST38 and were more related to hospital-onset than to community-onset infections and that the blaCTX-M gene may vary according to the ST.

  7. 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

  8. 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.

  9. Frontiers in cancer epidemiology: a challenge to the research community from the Epidemiology and Genomics Research Program at the National Cancer Institute.

    PubMed

    Khoury, Muin J; Freedman, Andrew N; Gillanders, Elizabeth M; Harvey, Chinonye E; Kaefer, Christie; Reid, Britt C; Rogers, Scott; Schully, Sheri D; Seminara, Daniela; Verma, Mukesh

    2012-07-01

    The Epidemiology and Genomics Research Program (EGRP) at the National Cancer Institute (NCI) is developing scientific priorities for cancer epidemiology research in the next decade. We would like to engage the research community and other stakeholders in a planning effort that will include a workshop in December 2012 to help shape new foci for cancer epidemiology research. To facilitate the process of defining the future of cancer epidemiology, we invite the research community to join in an ongoing web-based conversation at http://blog-epi.grants.cancer.gov/ to develop priorities and the next generation of high-impact studies. ©2012 AACR

  10. Genome-wide association mapping of partial resistance to Phytophthora sojae in soybean plant introductions from the Republic of Korea.

    PubMed

    Schneider, Rhiannon; Rolling, William; Song, Qijian; Cregan, Perry; Dorrance, Anne E; McHale, Leah K

    2016-08-11

    Phytophthora root and stem rot is one of the most yield-limiting diseases of soybean [Glycine max (L.) Merr], caused by the oomycete Phytophthora sojae. Partial resistance is controlled by several genes and, compared to single gene (Rps gene) resistance to P. sojae, places less selection pressure on P. sojae populations. Thus, partial resistance provides a more durable resistance against the pathogen. In previous work, plant introductions (PIs) originating from the Republic of Korea (S. Korea) have shown to be excellent sources for high levels of partial resistance against P. sojae. Resistance to two highly virulent P. sojae isolates was assessed in 1395 PIs from S. Korea via a greenhouse layer test. Lines exhibiting possible Rps gene immunity or rot due to other pathogens were removed and the remaining 800 lines were used to identify regions of quantitative resistance using genome-wide association mapping. Sixteen SNP markers on chromosomes 3, 13 and 19 were significantly associated with partial resistance to P. sojae and were grouped into seven quantitative trait loci (QTL) by linkage disequilibrium blocks. Two QTL on chromosome 3 and three QTL on chromosome 19 represent possible novel loci for partial resistance to P. sojae. While candidate genes at QTL varied in their predicted functions, the coincidence of QTLs 3-2 and 13-1 on chromosomes 3 and 13, respectively, with Rps genes and resistance gene analogs provided support for the hypothesized mechanism of partial resistance involving weak R-genes. QTL contributing to partial resistance towards P. sojae in soybean germplasm originating from S. Korea were identified. The QTL identified in this study coincide with previously reported QTL, Rps genes, as well as novel loci for partial resistance. Molecular markers associated with these QTL can be used in the marker-assisted introgression of these alleles into elite cultivars. Annotations of genes within QTL allow hypotheses on the possible mechanisms of partial

  11. 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

  12. Genomic Epidemiology of Hypervirulent Serogroup W, ST-11 Neisseria meningitidis

    PubMed Central

    Mustapha, Mustapha M.; Marsh, Jane W.; Krauland, Mary G.; Fernandez, Jorge O.; de Lemos, Ana Paula S.; Dunning Hotopp, Julie C.; Wang, Xin; Mayer, Leonard W.; Lawrence, Jeffrey G.; Hiller, N. Luisa; Harrison, Lee H.

    2015-01-01

    Neisseria meningitidis is a leading bacterial cause of sepsis and meningitis globally with dynamic strain distribution over time. Beginning with an epidemic among Hajj pilgrims in 2000, serogroup W (W) sequence type (ST) 11 emerged as a leading cause of epidemic meningitis in the African ‘meningitis belt’ and endemic cases in South America, Europe, Middle East and China. Previous genotyping studies were unable to reliably discriminate sporadic W ST-11 strains in circulation since 1970 from the Hajj outbreak strain (Hajj clone). It is also unclear what proportion of more recent W ST-11 disease clusters are caused by direct descendants of the Hajj clone. Whole genome sequences of 270 meningococcal strains isolated from patients with invasive meningococcal disease globally from 1970 to 2013 were compared using whole genome phylogenetic and major antigen-encoding gene sequence analyses. We found that all W ST-11 strains were descendants of an ancestral strain that had undergone unique capsular switching events. The Hajj clone and its descendants were distinct from other W ST-11 strains in that they shared a common antigen gene profile and had undergone recombination involving virulence genes encoding factor H binding protein, nitric oxide reductase, and nitrite reductase. These data demonstrate that recent acquisition of a distinct antigen-encoding gene profile and variations in meningococcal virulence genes was associated with the emergence of the Hajj clone. Importantly, W ST-11 strains unrelated to the Hajj outbreak contribute a significant proportion of W ST-11 cases globally. This study helps illuminate genomic factors associated with meningococcal strain emergence and evolution. PMID:26629539

  13. Comparative genomic analysis and characteristics of NCCP15740, the major type of enterotoxigenic Escherichia coli in Korea.

    PubMed

    Kwon, Taesoo; Chung, Si-Yun; Jung, Young-Hee; Jung, Su-Jin; Roh, Sang-Gyun; Park, Je-Seop; Kim, Cheorl-Ho; Kim, Won; Bak, Young-Seok; Cho, Seung-Hak

    2017-01-01

    Enterotoxigenic Escherichia coli (ETEC) cause infectious diarrhea and diarrheal death. However, the genetic properties of pathogenic strains vary spatially and temporally, making prevention and treatment difficult. In this study, the genomic features of the major type of ETEC in Korea from 2003 to 2011 were examined by whole-genome sequencing of strain NCCP15740, and a comparative genomic analysis was performed with O6 reference strains. The assembled genome size of NCCP15740 was 4,795,873 bp with 50.54% G+C content. Using rapid annotation using subsystem technology analysis, we predicted 4492 ORFs and 17 RNA genes. NCCP15740 was investigated for enterotoxin genes, colonization factor (CF) genes, serotype, multilocus sequence typing (MLST) profiles, and classical and nonclassical virulence factors. NCCP15740 belonged to the O6:H16 serotype and possessed enterotoxin genes encoding heat-stable toxin (STh) and heat-labile toxin (LT); 87.5% of the O6 serotype strains possessed both toxin types. NCCP15740 carried the colonization factors CS2 and CS3, whereas most O6 strains carried CS2-CS3-CS21 (79.2%). NCCP15740 harbored fewer virulence factors (59.4%) than the average observed in other O6 strains (62.0%). Interestingly, NCCP15740 did not harbor any nonclassical virulence genes. The major type of ETEC in Korea had the same MLST sequence type as that of isolates from the USA obtained in 2011 and 2014, but had different colonization factor types and virulence profiles. These results provide important information for the development of an ETEC vaccine candidate.

  14. Microarrays for Public Health: Genomic Epidemiology of Tuberculosis

    PubMed Central

    Shafi, Jamila; Andrew, Peter W.

    2002-01-01

    In response to a large local school-based outbreak of tuberculosis, we have been evaluating the utility of microarray bacterial genomic analysis in outbreak management. After initial comparison of the isolate from the index case with Mycobacterium tuberculosis H37Rv, it was possible to design robust PCRs directed towards strain-specific deletions. Rapid PCR analysis of isolates proved valuable in determining whether or not other isolates were compatible with the outbreak strain and further microarray studies revealed genetic markers that could be used to discriminate between locally circulating strains.We suggest that this approach forms the basis for developing rapid local genotyping schemes applicable to M. tuberculosis and that application to other pathogens warrants consideration. PMID:18629269

  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.

  16. 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

  17. Global Genomic Epidemiology of Salmonella enterica Serovar Typhimurium DT104

    SciTech Connect

    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.

    2016-03-04

    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], 1934 to 1962) and later became MDR DT104 in ~1972 (95% CI, 1972 to 1988) through horizontal transfer of the 13-kb Salmonella genomic island 1 (SGI1) MDR region into susceptible strains already containing SGI1. This was followed by multiple transmission events, initially from central Europe and later between several European countries. An independent transmission to the United States and another to Japan occurred, and from there MDR DT104 was probably transmitted to Taiwan and Canada. An independent acquisition of resistance genes took place in Thailand in ~1975 (95% CI, 1975 to 1990). In Denmark, WGS analysis provided evidence for transmission of the organism between herds of animals. Interestingly, the demographic history of Danish MDR DT104 provided evidence for the success of the program to eradicate Salmonella from pig herds in Denmark from 1996 to 2000. Finally, the results from this study refute several hypotheses on the evolution of DT104 and suggest that WGS may be useful in monitoring emerging clones and devising strategies for prevention of Salmonella infections.

  18. Global Genomic Epidemiology of Salmonella enterica Serovar Typhimurium DT104

    DOE PAGES

    Leekitcharoenphon, Pimlapas; Hendriksen, Rene S.; Le Hello, Simon; ...

    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

  19. Population genomic datasets describing the post-vaccine evolutionary epidemiology of Streptococcus pneumoniae

    PubMed Central

    Croucher, Nicholas J.; Finkelstein, Jonathan A.; Pelton, Stephen I.; Parkhill, Julian; Bentley, Stephen D.; Lipsitch, Marc; Hanage, William P.

    2015-01-01

    Streptococcus pneumoniae is common nasopharyngeal commensal bacterium and important human pathogen. Vaccines against a subset of pneumococcal antigenic diversity have reduced rates of disease, without changing the frequency of asymptomatic carriage, through altering the bacterial population structure. These changes can be studied in detail through using genome sequencing to characterise systematically-sampled collections of carried S. pneumoniae. This dataset consists of 616 annotated draft genomes of isolates collected from children during routine visits to primary care physicians in Massachusetts between 2001, shortly after the seven valent polysaccharide conjugate vaccine was introduced, and 2007. Also made available are a core genome alignment and phylogeny describing the overall population structure, clusters of orthologous protein sequences, software for inferring serotype from Illumina reads, and whole genome alignments for the analysis of closely-related sets of pneumococci. These data can be used to study both bacterial evolution and the epidemiology of a pathogen population under selection from vaccine-induced immunity. PMID:26528397

  20. 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

  1. 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. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

  2. Multiple Introductions of Zika Virus into the United States Revealed Through Genomic Epidemiology

    DTIC Science & Technology

    2017-02-02

    Multiple introductions of Zika virus into the United States revealed through genomic epidemiology Nathan D Grubaugh1*, Jason T Ladner2,*, Moritz UG...042 DISTRIBUTION STATEMENT A: Approved for public release; distribution is unlimited. UNCLASSIFIED Zika virus (ZIKV) is currently causing an...Medical Research Institute of Infectious Diseases (USAMRIID) Office of Human Use and Ethics and determined not to require IRB review. Florida Zika

  3. Multiple Introductions of Zika Virus into the United States Revealed through Genomic Epidemiology

    DTIC Science & Technology

    2017-02-09

    Multiple introductions of Zika virus into the United States revealed through genomic epidemiology Nathan D Grubaugh1*, Jason T Ladner2,*, Moritz UG...047 DISTRIBUTION STATEMENT A: Approved for public release; distribution is unlimited. UNCLASSIFIED Zika virus (ZIKV) is currently causing an...Medical Research Institute of Infectious Diseases (USAMRIID) Office of Human Use and Ethics and determined not to require IRB review. Florida Zika

  4. Molecular-based surveillance of campylobacteriosis in New Zealand--from source attribution to genomic epidemiology.

    PubMed

    Muellner, P; Pleydell, E; Pirie, R; Baker, M G; Campbell, D; Carter, P E; French, N P

    2013-01-17

    Molecular-based surveillance of campylobacteriosis in New Zealand contributed to the implementation of interventions that led to a 50% reduction in notified and hospitalised cases of the country's most important zoonosis. From a pre-intervention high of 384 per 100,000 population in 2006, incidence dropped by 50% in 2008; a reduction that has been sustained since. This article illustrates many aspects of the successful use of molecular-based surveillance, including the distinction between control-focused and strategy-focused surveillance and advances in source attribution. We discuss how microbial genetic data can enhance the understanding of epidemiological explanatory and response variables and thereby enrich the epidemiological analysis. Sequence data can be fitted to evolutionary and epidemiological models to gain new insights into pathogen evolution, the nature of associations between strains of pathogens and host species, and aspects of between-host transmission. With the advent of newer sequencing technologies and the availability of rapid, high-coverage genome sequence data, such techniques may be extended and refined within the emerging discipline of genomic epidemiology. The aim of this article is to summarise the experience gained in New Zealand with molecular-based surveillance of campylobacteriosis and to discuss how this experience could be used to further advance the use of molecular tools in surveillance.

  5. Complete genome sequences of three rabies viruses isolated from rabid raccoon dogs and a cow in Korea.

    PubMed

    Oem, Jae-Ku; Kim, Seong-Hee; Kim, Yeon-Hee; Lee, Myoung-Heon; Lee, Kyoung-Ki

    2013-12-01

    The complete genomes of three rabies viruses (BD0406CC, BV9901PJ, and 08F40) of two raccoon dogs (Nyctereutes procyonoides koreensis) and a cow were determined. The genomic organization is typical of rabies viruses, and the open reading frames of the N, P, M, G, and L genes are 1,353, 894, 609, 1,575, and 6,384 bases in length, respectively. The full genome length of the three strains was 11,928 nucleotides, and the sequence similarity between the rabies viruses at the nucleotide level was 98.5-99.5%. Sequence comparisons indicated that these rabies viruses belong to the "Arctic and Arctic-like" group, with high homology to the Eurasian cluster. All Korean strains were clustered with the Mongolia strains, which belong to Arctic-like 1 clade. The 08F40 and BD0406CC strains were constructed with rabies virus strains isolated in Gangwon province. The BV9901PJ strain was closely related to strains isolated in Gyeonggi province in Korea. Three strains were more dependent upon geographical distribution and time period than host species. Complete genome sequencing of different host-origin rabies viruses will provide information that should contribute to understanding the transmission cycle and genetic variability of rabies from different hosts.

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

    PubMed Central

    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.

    2014-01-01

    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. PMID:24394697

  7. Draft Genome Sequence of Fusobacterium nucleatum subsp. animalis ChDC F324, Isolated from a Human Subgingival Plaque in the Republic of Korea

    PubMed Central

    Park, Soon-Nang; Cho, Eugene; Kim, Hwa-Sook; Kim, Dae-Soo; Jung, Jaeeun; Baek, Jeong-Hun; Kyong Lim, Yun; Jo, Eojin; Chang, Young-Hyo; Hwan Shin, Jeong; Choi, Sang-Haeng; Kang, Jihee; Choi, YongUn; Kong, Si-Won; Han, Sang-Eun; Park, Hong-Seog; Kim, Hongik

    2013-01-01

    Five subspecies of Fusobacterium nucleatum have been classified: animalis, nucleatum, polymorphum, vincentii, and fusiforme. F. nucleatum subsp. animalis ChDC F324 (KCOM 1325) was isolated from a human subgingival plaque in the Republic of Korea. Here, we report the draft genome sequence of the strain. PMID:24336380

  8. Draft Genome Sequences of Pectobacterium carotovorum subsp. actinidiae ICMP 19971 and ICMP 19972, Two Strains Isolated from Actinidia chinensis with Symptoms of Summer Canker in South Korea.

    PubMed

    Visnovsky, Sandra B; Panda, Preetinanda; Taylor, Robert; Pitman, Andrew R

    2017-04-06

    Pectobacterium carotovorum subsp. actinidiae is the causal agent of summer canker in kiwifruit plants in South Korea. We report here the draft genome sequences of two P. carotovorum subsp. actinidiae strains, ICMP 19971 and ICMP 19972, which were originally isolated from Actinidia chinensis with symptoms of summer canker. These genome sequences will aid in the identification of genetic traits associated with their unusual capacity to cause canker and help understanding of the threat these exotic enterobacteria pose to the New Zealand kiwifruit industry.

  9. Comparative genomic fingerprinting of Campylobacter: application in routine public health surveillance and epidemiological investigations.

    PubMed

    Schleihauf, E; Mutschall, S; Billard, B; Taboada, E N; Haldane, D

    2017-01-01

    A subtyping methodology for Campylobacter, Comparative Genomic Fingerprinting (CGF40), has been described recently. The objective of this study was to assess the utility of CGF40 as a tool to enhance routine public health surveillance of campylobacteriosis. Isolates of Campylobacter from across the province were requested and sent for CGF40 subtyping. Epidemiological data from cases reported to public health officials in Nova Scotia, Canada, from January 2012 to March 2015 were linked with blinded CGF40 subtyping results. CGF40 was epidemiologically valid; subtyping discerned known epidemiologically related isolates and augmented case-finding. Predominant sources and locations of subtype detection from the national reference database showed some study subtypes were rare and even novel to the database, while others were more commonly identified over multiple years and with exposures locally and internationally. A case-case study design was applied to examine risk factors for the most common CGF40 subtypes detected. Differences in the epidemiology of different CGF40 subtypes were observed. Statistically significant associations were noted for specific subtypes with rural residence, local exposure, contact with a pet dog or cat, contact with chickens, and drinking unpasteurized milk. With prospective use, CGF40 could potentially identify unrecognized outbreaks and contribute to epidemiological investigations of case clusters.

  10. Straight from the Horse's "Mouth": Genomic Epidemiology of an Icelandic Equine Epidemic.

    PubMed

    Davies, Mark R

    2017-10-10

    Despite tight biosecurity measures, an outbreak of respiratory disease rapidly spread across the Icelandic equine population in 2010. Horse transportation was brought to a halt in order to contain the spread of the infectious agent. In a recent article, Björnsdóttir and colleagues (S. Björnsdóttir et al., mBio 8:e00826-17, 2017, https://doi.org/10.1128/mBio.00826-17) employ the power and resolution of "genomic epidemiology," the combination of whole genomic sequencing and epidemiological approaches, to examine the source and spread of the outbreak. Intriguingly, the outbreak was not viral in origin, but linked to a bacterial "commensal" Streptococcus equi subsp. zooepidemicus infection. A national sampling strategy coupled with population genomics revealed that the outbreak was most likely driven by a S. equi subsp. zooepidemicus sequence type 209 (ST209) infection that spread nationally from a single source. This retrospective study demonstrates the power of genomics applied on a national scale to unravel the cause of a significant biosecurity threat. Copyright © 2017 Davies.

  11. Complete genome sequencing of a recombinant strain between human astrovirus antigen types 2 and 8 isolated from South Korea.

    PubMed

    Ha, Hyun-Ju; Lee, Sung-Geun; Cho, Han-Gil; Jin, Ji-Young; Lee, Jae Woong; Paik, Soon-Yong

    2016-04-01

    Human astroviruses (HAstVs) occur worldwide and are known to the causative agents of diarrhea in infants and elderly patients with immune dysfunction. This study aimed to identify recombinant HAstV strains and characterize rare genotypes. The full-length genome of a recombinant HAstV strain isolated from the stool sample of a patient with acute gastroenteritis from South Korea was amplified using three pairs of previously designed primers and seven newly designed primers. The recombinant HAstV was 6757-bp long and contained three sequential open reading frames (ORFs), designated as ORF1a (2781 bp), ORF1b (1548 bp), and ORF2 (2349 bp). Our findings suggested that a recombination event had occurred between ORF1b and ORF2 of the isolated strain, with a recombination breakpoint at 4081 bp. To our knowledge, this is the first study to reveal the complete nucleotide sequence of a recombinant HAstV strain from South Korea. Our study findings might be useful for identifying other recombinant HAstV strains and for developing vaccines against this pathogenic virus. Copyright © 2016 Elsevier B.V. All rights reserved.

  12. 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.

  13. The complete mitochondrial genome of the black star fat minnow (Rhynchocypris semotilus), an endemic and endangered fish of Korea.

    PubMed

    Yu, Jeong-Nam; Kim, Byung-Jik; Kim, Changmu; Yeo, Joo-Hong; Kim, Soonok

    2017-01-01

    The Black star fat minnow (Rhynchocypris semotilus) is an endemic and critically endangered freshwater fish in Korea. Its genome was 16 605 bp long and consisted of 13 protein-coding genes (PCG), two rRNA genes, 22 tRNA genes, and a control region. The gene order and the composition of R. semotilus were similar to that of most other vertebrates. Four overlapping regions in ATP8/ATP6, ATP6/COX3, ND4L/ND4, and ND5/ND6, among the 13 PCGs were found. The control region was located between the tRNA-Pro and tRNA-Phe genes and was determined to be 935 bp in length with the 3' end containing a 12 TA-repeat sequence. Phylogenetic analysis suggested that R. semotilus is most closely related to R. oxycephalus.

  14. 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

  15. Genome-wide mosaicism within Mycobacterium abscessus: evolutionary and epidemiological implications.

    PubMed

    Sapriel, Guillaume; Konjek, Julie; Orgeur, Mickael; Bouri, Laurent; Frézal, Lise; Roux, Anne-Laure; Dumas, Emilie; Brosch, Roland; Bouchier, Christiane; Brisse, Sylvain; Vandenbogaert, Mathias; Thiberge, Jean-Michel; Caro, Valérie; Ngeow, Yun Fong; Tan, Joon Liang; Herrmann, Jean-Louis; Gaillard, Jean-Louis; Heym, Beate; Wirth, Thierry

    2016-02-17

    In mycobacteria, conjugation differs from the canonical Hfr model, but is still poorly understood. Here, we quantified this evolutionary processe in a natural mycobacterial population, taking advantage of a large clinical strain collection of the emerging pathogen Mycobacterium abscessus (MAB). Multilocus sequence typing confirmed the existence of three M. abscessus subspecies, and unravelled extensive allelic exchange between them. Furthermore, an asymmetrical gene flow occurring between these main lineages was detected, resulting in highly admixed strains. Intriguingly, these mosaic strains were significantly associated with cystic fibrosis patients with lung infections or chronic colonization. Genome sequencing of those hybrid strains confirmed that half of their genomic content was remodelled in large genomic blocks, leading to original tri-modal 'patchwork' architecture. One of these hybrid strains acquired a locus conferring inducible macrolide resistance, and a large genomic insertion from a slowly growing pathogenic mycobacteria, suggesting an adaptive gene transfer. This atypical genomic architecture of the highly recombinogenic strains is consistent with the distributive conjugal transfer (DCT) observed in M. smegmatis. Intriguingly, no known DCT function was found in M. abscessus chromosome, however, a p-RAW-like genetic element was detected in one of the highly admixed strains. Taken together, our results strongly suggest that MAB evolution is sporadically punctuated by dramatic genome wide remodelling events. These findings might have far reaching epidemiological consequences for emerging mycobacterial pathogens survey in the context of increasing numbers of rapidly growing mycobacteria and M. tuberculosis co-infections.

  16. 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

    2016-07-27

    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.

  17. Epidemiology of Trichomoniasis in South Korea and Increasing Trend in Incidence, Health Insurance Review and Assessment 2009-2014

    PubMed Central

    Joo, So-Young; Goo, Youn-Kyoung; Ryu, Jae-Sook; Lee, Sang-Eun; Lee, Won Kee; Chung, Dong-Il; Hong, Yeonchul

    2016-01-01

    Trichomoniasis, which is caused by Trichomonas vaginalis, is one of the most common non-viral sexually transmitted infections; however, limited population-based data are available that describe patterns and trends of the disease. We summarized insurance claims of trichomoniasis cases reported during 2009–2014 to South Korea Health Insurance Review and Assessment Service. The average annual incidence in South Korea was 276.8 persons per 100,000 population, and a substantial sex-associated variation was observed. The incidence rate among female subjects trended upward over 6 years, that is, it increased from 501 in 2009 to 625.8 in 2014 per 100,000 female population, which indicates a 25% overall increase. This trend was sharpest in the ≥60 years group of female population. However, a 66% decrease in incidence rates was observed among male subjects (23.7 in 2009 to 15.7 in 2014 per 100,000 male population). Further, substantial decrease was observed in the ≥40 years groups of male population. The incidence of trichomoniasis varied across regions and was the highest in Jeju province of South Korea. Overall, as the incidence of trichomoniasis appears to have increased in South Korea during 2009–2014, the disease burden is increasing; hence, there is a need to better understand the disease transmission. PMID:27936227

  18. Epidemiology of Trichomoniasis in South Korea and Increasing Trend in Incidence, Health Insurance Review and Assessment 2009-2014.

    PubMed

    Joo, So-Young; Goo, Youn-Kyoung; Ryu, Jae-Sook; Lee, Sang-Eun; Lee, Won Kee; Chung, Dong-Il; Hong, Yeonchul

    2016-01-01

    Trichomoniasis, which is caused by Trichomonas vaginalis, is one of the most common non-viral sexually transmitted infections; however, limited population-based data are available that describe patterns and trends of the disease. We summarized insurance claims of trichomoniasis cases reported during 2009-2014 to South Korea Health Insurance Review and Assessment Service. The average annual incidence in South Korea was 276.8 persons per 100,000 population, and a substantial sex-associated variation was observed. The incidence rate among female subjects trended upward over 6 years, that is, it increased from 501 in 2009 to 625.8 in 2014 per 100,000 female population, which indicates a 25% overall increase. This trend was sharpest in the ≥60 years group of female population. However, a 66% decrease in incidence rates was observed among male subjects (23.7 in 2009 to 15.7 in 2014 per 100,000 male population). Further, substantial decrease was observed in the ≥40 years groups of male population. The incidence of trichomoniasis varied across regions and was the highest in Jeju province of South Korea. Overall, as the incidence of trichomoniasis appears to have increased in South Korea during 2009-2014, the disease burden is increasing; hence, there is a need to better understand the disease transmission.

  19. 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.

  20. Molecular epidemiology of a post-influenza pandemic outbreak of acute respiratory infections in Korea caused by human adenovirus type 3.

    PubMed

    Lee, Wan-Ji; Jung, Hee-Dong; Cheong, Hyang-Min; Kim, Kisoon

    2015-01-01

    An outbreak of upper respiratory tract infections associated with human adenovirus (HAdV) occurred on a national scale in Korea from September to December 2010, following a major H1N1 influenza pandemic. Data from the Korea Influenza and Respiratory Surveillance System (KINRESS) showed an unusually high positive rate accounting for up to 20% of all diagnosed cases. To determine the principal cause of the outbreak, direct polymerase chain reaction (PCR) amplification followed by sequence analysis targeting parts of the hexon gene of HAdV was performed. Serotypes of 1,007 PCR-diagnosed HAdV-positive samples from patients with an acute upper respiratory tract illness were determined and epidemiological characteristics including major aged group and clinical symptoms were analyzed. The principal symptom of HAdV infections was fever and the vulnerable aged group was 1-5 years old. Based on sequence analysis, HAdV-3 was the predominant serotype in the outbreak, with an incidence of 74.3%. From the beginning of 2010 until May, the major serotypes were HAdV-1, 2, and 5 (70-100%) in any given period. However, an outbreak dominated by HAdV-3 started between July and August and peaked in September. Phylogenetic analysis revealed that there was no genetic variation in HAdV-3. The results demonstrated that an outbreak of upper respiratory illness followed by H1N1 influenza pandemic in Korea was caused mainly by emerged HAdV-3. J. © 2014 Wiley Periodicals, Inc.

  1. Complete genome sequence of Hymenobacter sp. DG25B, a novel bacterium with gamma-radiation resistance isolated from soil in South Korea.

    PubMed

    Kim, Myung Kyum; Joo, Eun Sun; Lee, Seung-Yeol; Lee, Dae Sung; Srinivasan, Sathiyaraj; Jung, Hee-Young

    2016-01-10

    A Gram-negative, rod-shaped, non-motile, gamma and UV radiation resistant bacterium Hymenobacter radioresistens DG25B was isolated from a soil sample collected in South Korea. The complete genome sequence of H. radioresistens DG25B consists of one circular chromosome (3,874,646 bp). The bacterium was isolated from gamma ray irradiated soil and contains the genomic features of enzymes involved in the nucleotide excision repair (NER) pathway that protect the damaged DNA. The genome also contains other genes involved in the efficient removal of double-strand breaks (DSB) caused by the ionizing radiations. Copyright © 2015 Elsevier B.V. All rights reserved.

  2. 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.

  3. Epidemiologic Features of Animal Bite Cases Occurring in Rabies-Endemic Areas of Korea, 2005 to 2009

    PubMed Central

    Han, Myung Guk; Jung Sang, Ryou; Jeong, Young Eui; Ju, Young Ran; Cho, Jung Eun; Park, Jun-Sun

    2012-01-01

    Objectives Human rabies is a reemerging infectious disease in Korea. There was no human rabies case for 14 years until the disease had reoccurred in 1999. To prevent occurrence of human rabies, surveillance for animal bite patients in rabies endemic areas in Korea was conducted since 2005 as a part of a human rabies control program. The animal bite cases were analyzed to determine whether patients were treated according to the post-exposure prophylaxis (PEP) guideline of the Korea Centers for Disease Control and Prevention. Methods Information of animal bite cases that occurred from 2005 to 2009 in rabies high-risk regions were collected by cooperation with Regional Public Health Centers in 18 cities/districts of rabies endemic areas. Results A total of 2458 animal bite cases were reported. Dogs accounted for 86% of animal bites and 67% of the animals were not vaccinated against rabies virus. For PEP, among rabies-vaccinated animals, 92.7% were observed for clinical signs and 1.4% underwent necropsy. Among unvaccinated animals, 72.7% were observed for clinical signs and 4.1% underwent necropsy. The remaining animals were not available for examination. Of the animal bite patients, 32.5% received PEP and 51.6% were treated by first aid or by washing the wound. Conclusions Given that no human rabies cases were reported since 2005 and animal rabies was continuously reported in endemic areas of Korea, the human rabies control program implemented in 2005 appears to have a significant role in the prevention and control of human rabies. PMID:24159481

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

    PubMed

    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

    2015-12-01

    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. 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. 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: 16% group Y, 6% group W, and 3% group

  5. The Promise of Whole Genome Pathogen Sequencing for the Molecular Epidemiology of Emerging Aquaculture Pathogens.

    PubMed

    Bayliss, Sion C; Verner-Jeffreys, David W; Bartie, Kerry L; Aanensen, David M; Sheppard, Samuel K; Adams, Alexandra; Feil, Edward J

    2017-01-01

    Aquaculture is the fastest growing food-producing sector, and the sustainability of this industry is critical both for global food security and economic welfare. The management of infectious disease represents a key challenge. Here, we discuss the opportunities afforded by whole genome sequencing of bacterial and viral pathogens of aquaculture to mitigate disease emergence and spread. We outline, by way of comparison, how sequencing technology is transforming the molecular epidemiology of pathogens of public health importance, emphasizing the importance of community-oriented databases and analysis tools.

  6. The Promise of Whole Genome Pathogen Sequencing for the Molecular Epidemiology of Emerging Aquaculture Pathogens

    PubMed Central

    Bayliss, Sion C.; Verner-Jeffreys, David W.; Bartie, Kerry L.; Aanensen, David M.; Sheppard, Samuel K.; Adams, Alexandra; Feil, Edward J.

    2017-01-01

    Aquaculture is the fastest growing food-producing sector, and the sustainability of this industry is critical both for global food security and economic welfare. The management of infectious disease represents a key challenge. Here, we discuss the opportunities afforded by whole genome sequencing of bacterial and viral pathogens of aquaculture to mitigate disease emergence and spread. We outline, by way of comparison, how sequencing technology is transforming the molecular epidemiology of pathogens of public health importance, emphasizing the importance of community-oriented databases and analysis tools. PMID:28217117

  7. 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

  8. 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

    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; Jung, Ki-Suck

    2015-12-01

    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. This study covers a 2-year interval. One year was data collected retrospectively and the second year was prospectively obtained data. 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. 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.

  9. Genomic Epidemiology of Salmonella enterica Serotype Enteritidis based on Population Structure of Prevalent Lineages

    PubMed Central

    Desai, Prerak T.; den Bakker, Henk C.; Mikoleit, Matthew; Tolar, Beth; Trees, Eija; Hendriksen, Rene S.; Frye, Jonathan G.; Porwollik, Steffen; Weimer, Bart C.; Wiedmann, Martin; Weinstock, George M.; Fields, Patricia I.; McClelland, Michael

    2014-01-01

    Salmonella enterica serotype Enteritidis is one of the most commonly reported causes of human salmonellosis. Its low genetic diversity, measured by fingerprinting methods, has made subtyping a challenge. We used whole-genome sequencing to characterize 125 S. enterica Enteritidis and 3 S. enterica serotype Nitra strains. Single-nucleotide polymorphisms were filtered to identify 4,887 reliable loci that distinguished all isolates from each other. Our whole-genome single-nucleotide polymorphism typing approach was robust for S. enterica Enteritidis subtyping with combined data for different strains from 2 different sequencing platforms. Five major genetic lineages were recognized, which revealed possible patterns of geographic and epidemiologic distribution. Analyses on the population dynamics and evolutionary history estimated that major lineages emerged during the 17th–18th centuries and diversified during the 1920s and 1950s. PMID:25147968

  10. Epidemiological and clinical characteristics of community-acquired severe sepsis and septic shock: a prospective observational study in 12 university hospitals in Korea.

    PubMed

    Park, Dae Won; Chun, Byung Chul; Kim, June Myung; Sohn, Jang Wook; Peck, Kyong Ran; Kim, Yang Soo; Choi, Young Hwa; Choi, Jun Yong; Kim, Sang Il; Eom, Joong Sik; Kim, Hyo Youl; Song, Joon Young; Song, Young Goo; Choi, Hee Jung; Kim, Min Ja

    2012-11-01

    A prospective multicenter observational study was performed to investigate the epidemiology and outcomes of community-acquired severe sepsis and septic shock. Subjects included 1,192 adult patients admitted to the 22 participating intensive care units (ICUs) of 12 university hospitals in the Korean Sepsis Registry System from April, 2005 through February, 2009. Male accounted for 656 (55%) patients. Mean age was 65.0 ± 14.2 yr. Septic shock developed in 740 (62.1%) patients. Bacteremia was present in 422 (35.4%) patients. The 28-day and in-hospital mortality rates were 23.0% and 28.0%, respectively. Men were more likely to have comorbid illnesses and acute organ dysfunctions, and had higher mortality and clinical severity compared to women. While respiratory sources of sepsis were common in men, urinary sources were predominant in women. In the multivariate logistic regression analysis, cancer (odds ratio 1.89; 95% confidence interval 1.13-3.17), urinary tract infection (0.25; 0.13-0.46), APACHE II score (1.05; 1.02-1.09), SOFA score on day 1 (1.13; 1.06-1.21) and metabolic dysfunction (2.24, 1.45-3.45) were independent clinical factors for gender-related in-hospital mortality. This study provided epidemiological and clinical characteristics of community-acquired severe sepsis and septic shock in ICUs in Korea, and demonstrated the impact of clinical factors on gender difference in mortality.

  11. Draft genome sequence of the halophilic Halobacillus mangrovi KTB 131 isolated from Topan salt of the Jeon-nam in Korea.

    PubMed

    Woo, Mingyeong; Park, Sun-Hee; Park, Kyounghee; Park, Min-Kyu; Kim, Ji-Yeon; Lee, Han-Seung; Sohn, Jae Hak; Lee, Dong-Woo; Nam, Gaewon; Shin, Kee-Sun; Lee, Sang-Jae

    2017-12-01

    The draft genome sequence of the halophilic bacterium Halobacillus mangrovi KTB 131, isolated from Topan salt of the Jeon-nam in Korea, was established. The genome comprises 4,151,649 bp, with a G + C content of 41.6%. The strain displays a high number of genes responsible for secondary metabolite biosynthesis, transport, and catabolism compared to other Halobacillus bacterial genus members. Numerous genes responsible for various transport systems, solute accumulation, and aromatic/sulfur decomposition were detected. The first genomic analysis encourages further research on comparative genomics and potential biotechnological applications. The whole draft genome sequence of Halobacillus mangrovi KTB 131 is now available (Bioproject PRJNA380285).

  12. Genomic Epidemiology and Management of Salmonella in Island Ecosystems Used for Takahe Conservation.

    PubMed

    Grange, Zoë L; Biggs, Patrick J; Rose, Shanna P; Gartrell, Brett D; Nelson, Nicola J; French, Nigel P

    2017-03-30

    Translocation and isolation of threatened wildlife in new environments may have unforeseen consequences on pathogen transmission and evolution in host populations. Disease threats associated with intensive conservation management of wildlife remain speculative without gaining an understanding of pathogen dynamics in meta-populations and how location attributes may determine pathogen prevalence. We determined the prevalence and population structure of an opportunistic pathogen, Salmonella, in geographically isolated translocated sub-populations of an endangered New Zealand flightless bird, the takahe (Porphyrio hochstetteri). Out of the nine sub-populations tested, Salmonella was only isolated from takahe living on one private island. The apparent prevalence of Salmonella in takahe on the private island was 32% (95% CI 13-57%), with two serotypes, Salmonella Mississippi and Salmonella houtenae 40:gt-, identified. Epidemiological investigation of reservoirs on the private island and another island occupied by takahe identified environmental and reptile sources of S. Mississippi and S. houtenae 40:gt- on the private island. Single nucleotide polymorphism analysis of core genomes revealed low-level diversity among isolates belonging to the same serotype and little differentiation according to host and environmental source. The pattern observed may be representative of transmission between sympatric hosts and environmental sources, the presence of a common unsampled source, and/or evidence of a recent introduction into the ecosystem. This study highlights how genomic epidemiology can be used to ascertain and understand disease dynamics to inform the management of disease threats in endangered wildlife populations.

  13. Middle East respiratory syndrome coronavirus (MERS-CoV) outbreak in South Korea, 2015: epidemiology, characteristics and public health implications.

    PubMed

    Kim, K H; Tandi, T E; Choi, J W; Moon, J M; Kim, M S

    2017-02-01

    Since the first case of Middle East respiratory syndrome coronavirus (MERS-CoV) in South Korea was reported on 20(th) May 2015, there have been 186 confirmed cases, 38 deaths and 16,752 suspected cases. Previously published research on South Korea's MERS outbreak was limited to the early stages, when few data were available. Now that the outbreak has ended, albeit unofficially, a more comprehensive review is appropriate. Data were obtained through the MERS portal by the Ministry for Health and Welfare (MOHW) and Korea Centres for Disease Control and Prevention, press releases by MOHW, and reports by the MERS Policy Committee of the Korean Medical Association. Cases were analysed for general characteristics, exposure source, timeline and infection generation. Sex, age and underlying diseases were analysed for the 38 deaths. Beginning with the index case that infected 28 others, an in-depth analysis was conducted. The average age was 55 years, which was a little higher than the global average of 50 years. As in most other countries, more men than women were affected. The case fatality rate was 19.9%, which was lower than the global rate of 38.7% and the rate in Saudi Arabia (36.5%). In total, 184 patients were infected nosocomially and there were no community-acquired infections. The main underlying diseases were respiratory diseases, cancer and hypertension. The main contributors to the outbreak were late diagnosis, quarantine failure of 'super spreaders', familial care-giving and visiting, non-disclosure by patients, poor communication by the South Korean Government, inadequate hospital infection management, and 'doctor shopping'. The outbreak was entirely nosocomial, and was largely attributable to infection management and policy failures, rather than biomedical factors. Copyright © 2016 The Healthcare Infection Society. Published by Elsevier Ltd. All rights reserved.

  14. Descriptive Epidemiology of Patients Undergoing Total Hip Arthroplasty in Korea with Focus on Incidence of Femoroacetabular Impingement: Single Center Study

    PubMed Central

    2017-01-01

    We analyzed the causes leading to total hip arthroplasty (THA), aimed to clarify the incidence of femoroacetabular impingement (FAI) among the causes, and compared the incidence in Korea with those in other countries. From January 2000 to December 2014, 1,206 hips of 818 patients who underwent primary THA at our institute were reviewed retrospectively in terms of radiographs and electronic charts. The radiographs and radiographic parameters were reviewed and measured by 2 of the authors, who are orthopedic surgeons. Patients were categorized in terms of the causes leading to THA as primary osteoarthritis (OA), rheumatoid arthritis (RA), posttraumatic arthritis, post infectious arthritis, avascular necrosis (AVN) of the femoral head, fracture of the femoral head or neck, ankylosing spondylitis (AS), developmental dysplasia of the hip (DDH), Legg-Calvé-Perthes disease (LCPD), FAI, and others. There were 32 patients (3.91%) in the primary OA group, 41 (5.01%) in the RA group, 84 (10.27%) in the posttraumatic arthritis group, 39 (4.77%) in the post infectious arthritis group, 365 (44.62%) in the AVN group, 39 (4.77%) in the fracture group, 21 (2.57%) in the AS group, 52 (6.36%) in the DDH group, 71 (8.68%) in the LCPD group, 52 (6.36%) in the FAI group, and 22 (2.69%) in the ‘other’ group. The causes leading to THA in Korea differ from those in Western countries. FAI could be causes of severe secondary OA that requires THA in Korea, therefore symptomatic FAI should not be neglected. PMID:28244282

  15. Genome-Wide Identification of Host-Segregating Epidemiological Markers for Source Attribution in Campylobacter jejuni.

    PubMed

    Thépault, Amandine; Méric, Guillaume; Rivoal, Katell; Pascoe, Ben; Mageiros, Leonardos; Touzain, Fabrice; Rose, Valérie; Béven, Véronique; Chemaly, Marianne; Sheppard, Samuel K

    2017-04-01

    Campylobacter is among the most common worldwide causes of bacterial gastroenteritis. This organism is part of the commensal microbiota of numerous host species, including livestock, and these animals constitute potential sources of human infection. Molecular typing approaches, especially multilocus sequence typing (MLST), have been used to attribute the source of human campylobacteriosis by quantifying the relative abundance of alleles at seven MLST loci among isolates from animal reservoirs and human infection, implicating chicken as a major infection source. The increasing availability of bacterial genomes provides data on allelic variation at loci across the genome, providing the potential to improve the discriminatory power of data for source attribution. Here we present a source attribution approach based on the identification of novel epidemiological markers among a reference pan-genome list of 1,810 genes identified by gene-by-gene comparison of 884 genomes of Campylobacter jejuni isolates from animal reservoirs, the environment, and clinical cases. Fifteen loci involved in metabolic activities, protein modification, signal transduction, and stress response or coding for hypothetical proteins were selected as host-segregating markers and used to attribute the source of 42 French and 281 United Kingdom clinical C. jejuni isolates. Consistent with previous studies of British campylobacteriosis, analyses performed using STRUCTURE software attributed 56.8% of British clinical cases to chicken, emphasizing the importance of this host reservoir as an infection source in the United Kingdom. However, among French clinical isolates, approximately equal proportions of isolates were attributed to chicken and ruminant reservoirs, suggesting possible differences in the relative importance of animal host reservoirs and indicating a benefit for further national-scale attribution modeling to account for differences in production, behavior, and food consumption

  16. Complete Genome Sequence of an Avian Paramyxovirus Type 4 Strain Isolated from Domestic Duck at a Live Bird Market in South Korea.

    PubMed

    Tseren-Ochir, Erdene-Ochir; Yuk, Seong-Su; Kwon, Jung-Hoon; Noh, Jin-Yong; Hong, Woo-Tack; Jeong, Jei-Hyun; Jeong, Sol; Kim, Yu-Jin; Kim, Kyu-Jik; Lee, Ji-Ho; Kim, Jun-Beom; Lee, Joong-Bok; Park, Seung-Yong; Choi, In-Soo; Lee, Sang-Won; Song, Chang-Seon

    2017-05-18

    We report here the first full-genome sequence of an avian paramyxovirus type 4 (APMV-4) strain isolated from a domestic mallard duck at a live bird market in South Korea. Phylogenetic analyses provide genetic information on a new genetic clade, APMV-4, isolated from a domestic duck and evidence of APMV-4 exchange between poultry and wild birds. Copyright © 2017 Tseren-Ochir et al.

  17. 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

  18. A Comparative Analysis of the Lyve-SET Phylogenomics Pipeline for Genomic Epidemiology of Foodborne Pathogens.

    PubMed

    Katz, Lee S; Griswold, Taylor; Williams-Newkirk, Amanda J; Wagner, Darlene; Petkau, Aaron; Sieffert, Cameron; Van Domselaar, Gary; Deng, Xiangyu; Carleton, Heather A

    2017-01-01

    Modern epidemiology of foodborne bacterial pathogens in industrialized countries relies increasingly on whole genome sequencing (WGS) techniques. As opposed to profiling techniques such as pulsed-field gel electrophoresis, WGS requires a variety of computational methods. Since 2013, United States agencies responsible for food safety including the CDC, FDA, and USDA, have been performing whole-genome sequencing (WGS) on all Listeria monocytogenes found in clinical, food, and environmental samples. Each year, more genomes of other foodborne pathogens such as Escherichia coli, Campylobacter jejuni, and Salmonella enterica are being sequenced. Comparing thousands of genomes across an entire species requires a fast method with coarse resolution; however, capturing the fine details of highly related isolates requires a computationally heavy and sophisticated algorithm. Most L. monocytogenes investigations employing WGS depend on being able to identify an outbreak clade whose inter-genomic distances are less than an empirically determined threshold. When the difference between a few single nucleotide polymorphisms (SNPs) can help distinguish between genomes that are likely outbreak-associated and those that are less likely to be associated, we require a fine-resolution method. To achieve this level of resolution, we have developed Lyve-SET, a high-quality SNP pipeline. We evaluated Lyve-SET by retrospectively investigating 12 outbreak data sets along with four other SNP pipelines that have been used in outbreak investigation or similar scenarios. To compare these pipelines, several distance and phylogeny-based comparison methods were applied, which collectively showed that multiple pipelines were able to identify most outbreak clusters and strains. Currently in the US PulseNet system, whole genome multi-locus sequence typing (wgMLST) is the preferred primary method for foodborne WGS cluster detection and outbreak investigation due to its ability to name standardized

  19. A Comparative Analysis of the Lyve-SET Phylogenomics Pipeline for Genomic Epidemiology of Foodborne Pathogens

    PubMed Central

    Katz, Lee S.; Griswold, Taylor; Williams-Newkirk, Amanda J.; Wagner, Darlene; Petkau, Aaron; Sieffert, Cameron; Van Domselaar, Gary; Deng, Xiangyu; Carleton, Heather A.

    2017-01-01

    Modern epidemiology of foodborne bacterial pathogens in industrialized countries relies increasingly on whole genome sequencing (WGS) techniques. As opposed to profiling techniques such as pulsed-field gel electrophoresis, WGS requires a variety of computational methods. Since 2013, United States agencies responsible for food safety including the CDC, FDA, and USDA, have been performing whole-genome sequencing (WGS) on all Listeria monocytogenes found in clinical, food, and environmental samples. Each year, more genomes of other foodborne pathogens such as Escherichia coli, Campylobacter jejuni, and Salmonella enterica are being sequenced. Comparing thousands of genomes across an entire species requires a fast method with coarse resolution; however, capturing the fine details of highly related isolates requires a computationally heavy and sophisticated algorithm. Most L. monocytogenes investigations employing WGS depend on being able to identify an outbreak clade whose inter-genomic distances are less than an empirically determined threshold. When the difference between a few single nucleotide polymorphisms (SNPs) can help distinguish between genomes that are likely outbreak-associated and those that are less likely to be associated, we require a fine-resolution method. To achieve this level of resolution, we have developed Lyve-SET, a high-quality SNP pipeline. We evaluated Lyve-SET by retrospectively investigating 12 outbreak data sets along with four other SNP pipelines that have been used in outbreak investigation or similar scenarios. To compare these pipelines, several distance and phylogeny-based comparison methods were applied, which collectively showed that multiple pipelines were able to identify most outbreak clusters and strains. Currently in the US PulseNet system, whole genome multi-locus sequence typing (wgMLST) is the preferred primary method for foodborne WGS cluster detection and outbreak investigation due to its ability to name standardized

  20. Draft Genome Sequences of Pectobacterium carotovorum subsp. actinidiae ICMP 19971 and ICMP 19972, Two Strains Isolated from Actinidia chinensis with Symptoms of Summer Canker in South Korea

    PubMed Central

    Panda, Preetinanda; Taylor, Robert; Pitman, Andrew R.

    2017-01-01

    ABSTRACT Pectobacterium carotovorum subsp. actinidiae is the causal agent of summer canker in kiwifruit plants in South Korea. We report here the draft genome sequences of two P. carotovorum subsp. actinidiae strains, ICMP 19971 and ICMP 19972, which were originally isolated from Actinidia chinensis with symptoms of summer canker. These genome sequences will aid in the identification of genetic traits associated with their unusual capacity to cause canker and help understanding of the threat these exotic enterobacteria pose to the New Zealand kiwifruit industry. PMID:28385839

  1. 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.

  2. Clonality and Resistome Analysis of KPC-Producing Klebsiella pneumoniae Strain Isolated in Korea Using Whole Genome Sequencing

    PubMed Central

    Yong, Ji Hyun; Lee, Yeong Seon; Yoo, Jung Sik; Yong, Dongeun; Hong, Seong Geun; D'Souza, Roshan; Thomson, Kenneth S.; Lee, Kyungwon; Chong, Yunsop

    2014-01-01

    We analyzed the whole genome sequence and resistome of the outbreak Klebsiella pneumoniae strain MP14 and compared it with those of K. pneumoniae carbapenemase- (KPC-) producing isolates that showed high similarity in the NCBI genome database. A KPC-2-producing multidrug-resistant (MDR) K. pneumoniae clinical isolate was obtained from a patient admitted to a Korean hospital in 2011. The strain MP14 was resistant to all tested β-lactams including monobactam, amikacin, levofloxacin, and cotrimoxazole, but susceptible to tigecycline and colistin. Resistome analysis showed the presence of β-lactamase genes including blaKPC-2, blaSHV-11, blaTEM-169, and blaOXA-9. MP14 also possessed aac(6′-)Ib, aadA2, and aph(3′-)Ia as aminoglycoside resistance-encoding genes, mph(A) for macrolides, oqxA and oqxB for quinolone, catA1 for phenicol, sul1 for sulfonamide, and dfrA12 for trimethoprim. Both SNP tree and cgMLST analysis showed the close relatedness with the KPC producers (KPNIH strains) isolated from an outbreak in the USA and colistin-resistant strains isolated in Italy. The plasmid-scaffold genes in plasmids pKpQil, pKpQil-IT, pKPN3, or pKPN-IT were identified in MP14, KPNIH, and Italian strains. The KPC-2-producing MDR K. pneumoniae ST258 stain isolated in Korea was highly clonally related with MDR K. pneumoniae strains from the USA and Italy. Global spread of KPC-producing K. pneumoniae is a worrying phenomenon. PMID:25105122

  3. Clonality and Resistome analysis of KPC-producing Klebsiella pneumoniae strain isolated in Korea using whole genome sequencing.

    PubMed

    Lee, Yangsoon; Kim, Bong-Soo; Chun, Jongsik; Yong, Ji Hyun; Lee, Yeong Seon; Yoo, Jung Sik; Yong, Dongeun; Hong, Seong Geun; D'Souza, Roshan; Thomson, Kenneth S; Lee, Kyungwon; Chong, Yunsop

    2014-01-01

    We analyzed the whole genome sequence and resistome of the outbreak Klebsiella pneumoniae strain MP14 and compared it with those of K. pneumoniae carbapenemase- (KPC-) producing isolates that showed high similarity in the NCBI genome database. A KPC-2-producing multidrug-resistant (MDR) K. pneumoniae clinical isolate was obtained from a patient admitted to a Korean hospital in 2011. The strain MP14 was resistant to all tested β-lactams including monobactam, amikacin, levofloxacin, and cotrimoxazole, but susceptible to tigecycline and colistin. Resistome analysis showed the presence of β-lactamase genes including bla KPC-2, bla SHV-11, bla TEM-169, and bla OXA-9. MP14 also possessed aac(6'-)Ib, aadA2, and aph(3'-)Ia as aminoglycoside resistance-encoding genes, mph(A) for macrolides, oqxA and oqxB for quinolone, catA1 for phenicol, sul1 for sulfonamide, and dfrA12 for trimethoprim. Both SNP tree and cgMLST analysis showed the close relatedness with the KPC producers (KPNIH strains) isolated from an outbreak in the USA and colistin-resistant strains isolated in Italy. The plasmid-scaffold genes in plasmids pKpQil, pKpQil-IT, pKPN3, or pKPN-IT were identified in MP14, KPNIH, and Italian strains. The KPC-2-producing MDR K. pneumoniae ST258 stain isolated in Korea was highly clonally related with MDR K. pneumoniae strains from the USA and Italy. Global spread of KPC-producing K. pneumoniae is a worrying phenomenon.

  4. The complete mitochondrial genome of Sebastes pachycephalus (Scorpaenidae, Scorpaeniformes) from the East Sea, Korea.

    PubMed

    Jang, Yo-Soon; Park, Kwang-Jae; Kim, Ki-Yong; Kim, Sung

    2016-01-01

    Due to variations in coloration as well as other morphological features, the identification of Sebastes pachycephalus has been problematic. The complete mitogenome of S. pachycephalus was acquired using next-generation sequencing. The full genome was 16,415 base pairs (bp) in length, assembling two rRNAs, 22 tRNAs, one control region and 13 protein-coding genes (PCGs). The genome constitutes 27.9% A, 26.3% T, 17.2% G and 28.5% C, showing a slight AT bias (54.2%). All PCGs start with an ATG initial codon except COX1, which contains GTG. Most PCG stop codons were TAA, except for ND1 and ND3 (TAG) and Cytb (incomplete termination codon, T). All tRNAs showed the typical cloverleaf structure, except tRNA(Ser(AGY)), which lacks the DHU arm. The complete mitogenome of S. pachycephalus will help further identification and speciation analyses.

  5. 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.

  6. Genomic Epidemiology of USA300 Methicillin-Resistant Staphylococcus aureus in an Urban Community

    PubMed Central

    Popovich, Kyle J.; Snitkin, Evan; Green, Stefan J.; Aroutcheva, Alla; Hayden, Mary K.; Hota, Bala; Weinstein, Robert A.

    2016-01-01

    Background. In a community, it is unknown what factors account for transmission of methicillin-resistant Staphylococcus aureus (MRSA). We integrated whole genome sequencing (WGS) and epidemiologic data to identify factors associated with MRSA transmission networks in an urban community. Methods. WGS was performed on colonizing USA300 MRSA isolates from 74 individuals within 72 hours of admission to a public hospital in Chicago, IL. Single nucleotide variants (SNVs) were used to reconstruct the phylogeny of sequenced isolates, and epidemiologic data was overlaid to identify factors associated with transmission networks. Results. The maximum within-patient SNV difference for an individual with multisite colonization was 41 SNVs, with no systematic divergence among body sites. We observed a minimum of 7 SNVs and maximum of 153 SNVs between isolates from different individuals. We identified 4 pairs of individuals whose isolates were within 40 SNVs of each other. Putting our isolates in the context of previously sequenced USA300 isolates from other communities, we identified a 13-member group and two 4-member groups that represent samples from putative local transmission networks. Individuals in these groups were more likely to be African American, to be human immunodeficiency virus–infected, to reside in high detainee release areas, and to be current users of illicit drugs. Conclusions. Using WGS, we observed potential transmission networks in an urban community and that certain epidemiologic factors were associated with inclusion in these networks. Future work with contact tracing and advanced molecular diagnostics may allow for identification of MRSA “epicenters” in the community where interventions can be targeted. PMID:26347509

  7. Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011.

    PubMed

    Grad, Yonatan H; Lipsitch, Marc; Feldgarden, Michael; Arachchi, Harindra M; Cerqueira, Gustavo C; Fitzgerald, Michael; Godfrey, Paul; Haas, Brian J; Murphy, Cheryl I; Russ, Carsten; Sykes, Sean; Walker, Bruce J; Wortman, Jennifer R; Young, Sarah; Zeng, Qiandong; Abouelleil, Amr; Bochicchio, James; Chauvin, Sara; Desmet, Timothy; Gujja, Sharvari; McCowan, Caryn; Montmayeur, Anna; Steelman, Scott; Frimodt-Møller, Jakob; Petersen, Andreas M; Struve, Carsten; Krogfelt, Karen A; Bingen, Edouard; Weill, François-Xavier; Lander, Eric S; Nusbaum, Chad; Birren, Bruce W; Hung, Deborah T; Hanage, William P

    2012-02-21

    The degree to which molecular epidemiology reveals information about the sources and transmission patterns of an outbreak depends on the resolution of the technology used and the samples studied. Isolates of Escherichia coli O104:H4 from the outbreak centered in Germany in May-July 2011, and the much smaller outbreak in southwest France in June 2011, were indistinguishable by standard tests. We report a molecular epidemiological analysis using multiplatform whole-genome sequencing and analysis of multiple isolates from the German and French outbreaks. Isolates from the German outbreak showed remarkably little diversity, with only two single nucleotide polymorphisms (SNPs) found in isolates from four individuals. Surprisingly, we found much greater diversity (19 SNPs) in isolates from seven individuals infected in the French outbreak. The German isolates form a clade within the more diverse French outbreak strains. Moreover, five isolates derived from a single infected individual from the French outbreak had extremely limited diversity. The striking difference in diversity between the German and French outbreak samples is consistent with several hypotheses, including a bottleneck that purged diversity in the German isolates, variation in mutation rates in the two E. coli outbreak populations, or uneven distribution of diversity in the seed populations that led to each outbreak.

  8. 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.

  9. Clinical and epidemiological factors associated with methicillin resistance in community-onset invasive Staphylococcus aureus infections: prospective multicenter cross-sectional study in Korea.

    PubMed

    Kim, Eu Suk; Kim, Hong Bin; Kim, Gayeon; Kim, Kye-Hyung; Park, Kyung-Hwa; Lee, Shinwon; Choi, Young Hwa; Yi, Jongyoun; Kim, Chung Jong; Song, Kyoung-Ho; Choe, Pyoeng Gyun; Kim, Nam-Joong; Lee, Yeong-Seon; Oh, Myoung-Don

    2014-01-01

    Successful empirical therapy of Staphylococcus aureus infections requires the ability to predict methicillin resistance. Our aim was to identify predictors of methicillin resistance in community-onset (CO) invasive S. aureus infections. Sixteen hospitals across Korea participated in this study from May to December 2012. We prospectively included cases of S. aureus infection in which S. aureus was isolated from sterile clinical specimens ≤ 72 hours after hospitalization. Clinical and epidemiological data were gathered and compared in methicillin-resistant S. aureus (MRSA) and methicillin-susceptible S. aureus (MSSA) cases. Community-associated (CA) infections were defined as in previous studies. In total, there were 786 cases of community-onset S. aureus infection, 102 (13.0%) of which were CA-MRSA. In addition to known risk factors, exposure to 3rd generation cephalosporins in the past 6 months [odds ratio (OR), 1.922; 95% confidence interval (CI), 1.176-3.142] and close contact with chronically ill patients in the past month (OR, 2.647; 95% CI, 1.189-5.891) were independent risk factors for MRSA infection. However, no clinical predictors of CA-MRSA were identified. Methicillin resistance, CO infection, and appropriateness of empirical antibiotics were not significantly related to 30-day mortality. MRSA infection should be suspected in patients recently exposed to 3rd generation cephalosporins or chronically-ill patients. There were no reliable predictors of CA-MRSA infection, and mortality was not affected by methicillin resistance.

  10. Epidemiological characteristics of genital herpes and condyloma acuminata in patients presenting to urologic and gynecologic clinics in Korea.

    PubMed

    Lee, Choong Bum; Choe, Hyun-Sop; Hwang, Seong-Jin; Lee, Seung-Ju; Cho, Yong-Hyun

    2011-06-01

    As viral sexually transmitted infections (STIs) are hard to cure completely and because they recur frequently, the management of patients and the prevention of the spread of viral STIs are important, rather than focusing on their treatment, unlike the focus for bacterial STIs. Thus, their prevalence and epidemiological characteristics should be investigated first. This study examined the prevalence of genital herpes and condyloma acuminata in patients visiting urologic and gynecologic clinics and evaluated the epidemiological characteristics of these diseases through questionnaire surveys. Out of 167,767 patients, 1,585 were reported to have genital herpes and condyloma acuminata, and the prevalences of the two diseases were 0.58 and 0.37%, respectively. The percentage of patients with viral STIs as a proportion of the total number of patients with STIs including bacterial STIs, was 35.6%. While the prevalence of genital herpes was relatively higher in middle-aged patients, that of condyloma acuminata was observed to be higher in relatively young patients. Among the patients participating in the questionnaire survey, 39.5 and 21.0% responded that they had experienced recurrence of genital herpes and condyloma acuminata, respectively. In conclusion, because the prevalences of genital herpes and condyloma acuminata as viral STIs were not trivial compared to that of bacterial STIs, and because of their frequent recurrence, policies adjusted to the characteristics of these viral STIs and more studies on the management of recurrence are necessary.

  11. Pathway Analysis of Metabolic Syndrome Using a Genome-Wide Association Study of Korea Associated Resource (KARE) Cohorts

    PubMed Central

    Shim, Unjin; Kim, Han-Na; Sung, Yeon-Ah

    2014-01-01

    Metabolic syndrome (MetS) is a complex disorder related to insulin resistance, obesity, and inflammation. Genetic and environmental factors also contribute to the development of MetS, and through genome-wide association studies (GWASs), important susceptibility loci have been identified. However, GWASs focus more on individual single-nucleotide polymorphisms (SNPs), explaining only a small portion of genetic heritability. To overcome this limitation, pathway analyses are being applied to GWAS datasets. The aim of this study is to elucidate the biological pathways involved in the pathogenesis of MetS through pathway analysis. Cohort data from the Korea Associated Resource (KARE) was used for analysis, which include 8,842 individuals (age, 52.2 ± 8.9 years; body mass index, 24.6 ± 3.2 kg/m2). A total of 312,121 autosomal SNPs were obtained after quality control. Pathway analysis was conducted using Meta-analysis Gene-Set Enrichment of Variant Associations (MAGENTA) to discover the biological pathways associated with MetS. In the discovery phase, SNPs from chromosome 12, including rs11066280, rs2074356, and rs12229654, were associated with MetS (p < 5 × 10-6), and rs11066280 satisfied the Bonferroni-corrected cutoff (unadjusted p < 1.38 × 10-7, Bonferroni-adjusted p < 0.05). Through pathway analysis, biological pathways, including electron carrier activity, signaling by platelet-derived growth factor (PDGF), the mitogen-activated protein kinase kinase kinase cascade, PDGF binding, peroxisome proliferator-activated receptor (PPAR) signaling, and DNA repair, were associated with MetS. Through pathway analysis of MetS, pathways related with PDGF, mitogen-activated protein kinase, and PPAR signaling, as well as nucleic acid binding, protein secretion, and DNA repair, were identified. Further studies will be needed to clarify the genetic pathogenesis leading to MetS. PMID:25705158

  12. Occurrence of Diverse AbGRI1-Type Genomic Islands in Acinetobacter baumannii Global Clone 2 Isolates from South Korea.

    PubMed

    Kim, Dae Hun; Jung, Sook-In; Kwon, Ki Tae; Ko, Kwan Soo

    2017-02-01

    In this study, we analyzed the frequency of the AbGRI1-type genomic island (GI) and its association with genotypes. We obtained 130 Acinetobacter baumannii isolates causing bloodstream infections from patients in South Korea. Antimicrobial susceptibility testing and multilocus sequence typing were performed. The presence of AbGRI1-type GIs and their structures were determined by sequential PCR and sequencing. Ninety-eight isolates (75.3%) representing 14 sequence types (STs) belonged to clonal complex 208 (CC208), corresponding to global clone 2 (GC2). AbGRI1-type GIs interrupted the comM gene in 107 isolates (82.4%). Four types of GIs were identified: Tn6022 (50 isolates; 46.7%), AbaR4 (23 isolates; 21.5%), Tn6166 (10 isolates; 9.3%), and Tn6166/Tn2006 (24 isolates; 22.4%). In the 50 isolates with Tn6022, Tn2006 or Tn2008B, both containing ISAba1-blaOXA-23, was present in sites other than GIs in 3 or 28 isolates, respectively. In the 10 isolates with Tn6166, Tn2008B was identified in one isolate. AbGRI1-type GIs were identified nearly exclusively in CC208 isolates, with the exception of nine non-CC208 isolates (AbaR4 in eight ST229 isolates and Tn6022 in one ST1244 isolate). Within CC208 isolates, there was evidence of frequent recombination events, in both housekeeping genes and AbGRI1-type GIs, contributing to genotype diversification and the emergence of carbapenem resistance.

  13. 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. Copyright © 2015 Elsevier B.V. All rights reserved.

  14. Sympatric distribution of three human Taenia tapeworms collected between 1935 and 2005 in Korea.

    PubMed

    Jeon, Hyeong-Kyu; Kim, Kyu-Heon; Chai, Jong-Yil; Yang, Hyun-Jong; Rim, Han-Jong; Eom, Keeseon S

    2008-12-01

    Taeniasis has been known as one of the prevalent parasitic infections in Korea. Until recently, Taenia saginata had long been considered a dominant, and widely distributed species but epidemiological profiles of human Taenia species in Korea still remain unclear. In order to better understand distribution patterns of human Taenia tapeworms in Korea, partial nucleotide sequences of mitochondrial cox1 and ITS2 (internal transcribed spacer 2) were determined, along with morphological examinations, on 68 Taenia specimens obtained from university museum collections deposited since 1935. Genomic DNA was extracted from formalin-preserved specimens. Phylogenetic relationships among the genotypes (cox1 haplotype) detected in this study were inferred using the neighbor-joining method as a tree building method. Morphological and genetic analyses identified 3 specimens as T. solium, 51 specimens as T. asiatica, and 14 specimens as T. saginata. Our results indicate that all 3 Taenia tapeworms are sympatrically distributed in Korea with T. asiatica dominating over T. saginata and T. solium.

  15. 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.

  16. 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

  17. Prevalence and molecular epidemiology of vancomycin-resistant enterococci (VRE) strains isolated from animals and humans in Korea.

    PubMed

    Song, Joon Young; Hwang, In Sook; Eom, Joong Sik; Cheong, Hee Jin; Bae, Won Ki; Park, Yong Ho; Kim, Woo Joo

    2005-03-01

    To assess the possibility of VRE transmission from animals to humans, we studied the prevalence of vancomycin-resistant enterococci (VRE) in farm animals, raw chicken meat, and healthy people. We then determined the molecular relatedness of VRE isolates between animals and humans in Korea. We aimed to isolate VRE from 150 enterococci specimens of farm animals, 15 raw chicken meat samples, and stools from 200 healthy people. Species differentiation was done with conventional biochemical tests. Vancomycin resistance genotyping was done by polymerase chain reaction (PCR). Using the agar dilution method, antimicrobial susceptibility was tested for 8 antimicrobials and pulsed-field gel electrophoresis (PFGE) was done to evaluate the molecular relatedness of VRE isolates. The prevalence of VRE was 14.7% (22/150) in farm animal specimens, 1% (2/200) in healthy people, and 60% (9/15) in raw chicken meat. Of 22 animal VRE isolates, 1 vanA E. faecium, 15 vanC1 E. gallinarum, and 6 vanC2 E. casseliflavus were identified. All of the 9 VRE from raw chicken meat and all of the 20 clinical VRE strains were vanA E. faecium. However, in healthy people, only 2 vanC2 E. casseliflavus were isolated. These showed low-level resistance to vancomycin and susceptibility to teicoplanin. However, 9 VRE strains from raw chicken meat had high-level resistance to vancomycin (MIC(50,90): >128 microg/mL), teicoplanin (MIC(50,90): >128 microg/mL), ampicillin (MIC(50,90): >128 nicrog/mL), erythromycin (MIC(50.90): >128 microg/mL), and tetracycline (MIC(50/90): 128/>128 microg/mL). This study demonstrated little evidence of VRE colonization in healthy people despite high recovery of VRE among raw chicken meat. It is suggested that there is little evidence of VRE transmission from animals to healthy people. However, we assumed that there exists the possibility of VRE contamination during the processing of chicken meat.

  18. Prevalence and Molecular Epidemiology of Vancomycin-Resistant Enterococci (VRE) Strains Isolated from Animals and Humans in Korea

    PubMed Central

    Song, Joon Young; Hwang, In Sook; Eom, Joong Sik; Cheong, Hee Jin; Bae, Won Ki; Park, Yong Ho

    2005-01-01

    Background To assess the possibility of VRE transmission from animals to humans, we studied the prevalence of vancomycin-resistant enterococci (VRE) in farm animals, raw chicken meat, and healthy people. We then determined the molecular relatedness of VRE isolates between animals and humans in Korea. Methods We aimed to isolate VRE from 150 enterococci specimens of farm animals, 15 raw chicken meat samples, and stools from 200 healthy people. Species differentiation was done with conventional biochemical tests. Vancomycin resistance genotyping was done by polymerase chain reaction (PCR). Using the agar dilution method, antimicrobial susceptibility was tested for 8 antimicrobials and pulsed-field gel electrophoresis (PFGE) was done to evaluate the molecular relatedness of VRE isolates. Results The prevalence of VRE was 14.7% (22/150) in farm animal specimens, 1% (2/200) in healthy people, and 60% (9/15) in raw chicken meat. Of 22 animal VRE isolates, 1 vanA E. faecium, 15 vanC1 E. gallinarum, and 6 vanC2 E. casseliflavus were identified. All of the 9 VRE from raw chicken meat and all of the 20 clinical VRE strains were vanA E. faecium. However, in healthy people, only 2 vanC2 E. casseliflavus were isolated. These showed low-level resistance to vancomycin and susceptibility to teicoplanin. However, 9 VRE strains from raw chicken meat had high-level resistance to vancomycin (MIC50,90: >128 µg/mL), teicoplanin (MIC50,90: >128 µg/mL), ampicillin (MIC50,90: >128 µg/mL), erythromycin (MIC50,90: >128 µg/mL), and tetracycline (MIC50,90: 128/>128 µg/mL). Conclusion This study demonstrated little evidence of VRE colonization in healthy people despite high recovery of VRE among raw chicken meat. It is suggested that there is little evidence of VRE transmission from animals to healthy people. However, we assumed that there exists the possibility of VRE contamination during the processing of chicken meat. PMID:15906954

  19. Genomic Profile of Chronic Lymphocytic Leukemia in Korea Identified by Targeted Sequencing

    PubMed Central

    Park, Si Nae; Huh, Sunghoon; Im, Kyongok; Choi, Sungbin; Chung, Hye Yoon; Huh, JooRyung; Seo, Eul-Ju; Lee, Je-Hwan; Bang, Duhee; Lee, Dong Soon

    2016-01-01

    Chronic lymphocytic leukemia (CLL) is extremely rare in Asian countries and there has been one report on genetic changes for 5 genes (TP53, SF3B1, NOTCH1, MYD88, and BIRC3) by Sanger sequencing in Chinese CLL. Yet studies of CLL in Asian countries using Next generation sequencing have not been reported. We aimed to characterize the genomic profiles of Korean CLL and to find out ethnic differences in somatic mutations with prognostic implications. We performed targeted sequencing for 87 gene panel using next-generation sequencing along with G-banding and fluorescent in situ hybridization (FISH) for chromosome 12, 13q14.3 deletion, 17p13 deletion, and 11q22 deletion. Overall, 36 out of 48 patients (75%) harbored at least one mutation and mean number of mutation per patient was 1.6 (range 0–6). Aberrant karyotypes were observed in 30.4% by G-banding and 66.7% by FISH. Most recurrent mutation (>10% frequency) was ATM (20.8%) followed by TP53 (14.6%), SF3B1 (10.4%), KLHL6 (8.3%), and BCOR (6.25%). Mutations of MYD88 was associated with moderate adverse prognosis by multiple comparisons (P = 0.055). Mutation frequencies of MYD88, SAMHD1, EGR2, DDX3X, ZMYM3, and MED12 showed similar incidence with Caucasians, while mutation frequencies of ATM, TP53, KLHL6, BCOR and CDKN2A tend to be higher in Koreans than in Caucasians. Especially, ATM mutation showed 1.5 fold higher incidence than Caucasians, while mutation frequencies of SF3B1, NOTCH1, CHD2 and POT1 tend to be lower in Koreans than in Caucasians. However, mutation frequencies between Caucasians and Koreans were not significantly different statistically, probably due to low number of patients. Collectively, mutational profile and adverse prognostic genes in Korean CLL were different from those of Caucasians, suggesting an ethnic difference, while profile of cytogenetic aberrations was similar to those of Caucasians. PMID:27959900

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

    PubMed

    Azarian, Taj; 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

  1. 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

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

    PubMed

    Fitzpatrick, Margaret A; Ozer, Egon A; Hauser, Alan R

    2016-03-01

    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.

  3. Genome wide association for substance dependence: convergent results from epidemiologic and research volunteer samples

    PubMed Central

    Johnson, Catherine; Drgon, Tomas; Liu, Qing-Rong; Zhang, Ping-Wu; Walther, Donna; Li, Chuan-Yun; Anthony, James C; Ding, Yulan; Eaton, William W; Uhl, George R

    2008-01-01

    Background Dependences on addictive substances are substantially-heritable complex disorders whose molecular genetic bases have been partially elucidated by studies that have largely focused on research volunteers, including those recruited in Baltimore. Maryland. Subjects recruited from the Baltimore site of the Epidemiological Catchment Area (ECA) study provide a potentially-useful comparison group for possible confounding features that might arise from selecting research volunteer samples of substance dependent and control individuals. We now report novel SNP (single nucleotide polymorphism) genome wide association (GWA) results for vulnerability to substance dependence in ECA participants, who were initially ascertained as members of a probability sample from Baltimore, and compare the results to those from ethnically-matched Baltimore research volunteers. Results We identify substantial overlap between the home address zip codes reported by members of these two samples. We find overlapping clusters of SNPs whose allele frequencies differ with nominal significance between substance dependent vs control individuals in both samples. These overlapping clusters of nominally-positive SNPs identify 172 genes in ways that are never found by chance in Monte Carlo simulation studies. Comparison with data from human expressed sequence tags suggests that these genes are expressed in brain, especially in hippocampus and amygdala, to extents that are greater than chance. Conclusion The convergent results from these probability sample and research volunteer sample datasets support prior genome wide association results. They fail to support the idea that large portions of the molecular genetic results for vulnerability to substance dependence derive from factors that are limited to research volunteers. PMID:19094236

  4. 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

  5. In vitro fluconazole and voriconazole susceptibilities of Candida bloodstream isolates in Korea: use of the CLSI and EUCAST epidemiological cutoff values.

    PubMed

    Jang, Min Joong; Shin, Jong Hee; Lee, Wee Gyo; Kim, Mi-Na; Lee, Kyungwon; Lee, Hye Soo; Lee, Mi-Kyung; Chang, Chulhun L; Jang, Hee-Chang; Song, Eun Song; Kim, Soo Hyun; Shin, Myung-Geun; Suh, Soon-Pal; Ryang, Dong-Wook

    2013-05-01

    At present, the clinical breakpoints (CBPs) of both fluconazole and voriconazole are available only for 3 common Candida species in the Clinical and Laboratory Standards Institute (CLSI) and the European Committee on Antimicrobial Susceptibility Testing (EUCAST) methods. Epidemiological cutoff values (ECVs) were recently applied to both methods to detect the emergence of acquired resistance (i.e., non-wild-type isolates) among 5 common Candida species. We performed a nationwide study to determine the fluconazole and voriconazole susceptibility of Candida bloodstream isolates (BSIs) using both the CLSI and EUCAST methods. A total of 423 BSIs of 5 Candida species were collected from 8 hospitals. The azole susceptibilities were assessed on the basis of the species-specific CBPs and ECVs. Of the 341 BSIs of 3 common Candida species (i.e., C. albicans, C. tropicalis, and C. parapsilosis), 0.3% and 0.9%, 0.0% and 1.5% of isolates were categorized as fluconazole and voriconazole resistant according to the CLSI and EUCAST CBPs, respectively. Of 423 total BSIs, 1.4% and 2.6% had fluconazole minimum inhibitory concentrations (MICs) exceeding the ECVs according to the CLSI and EUCAST, respectively; 1.0% and 2.1% had voriconazole MICs exceeding the ECVs according to the CLSI and EUCAST, respectively. Categorical agreement between the methods using ECVs was 98.3% for fluconazole and 98.3% for voriconazole. The EUCAST and CLSI methods using ECVs provide highly concordant results. Moreover, non-wild-type isolates with possibly acquired azole resistance were rare among the BSIs of 5 common Candida species in Korea.

  6. In Vitro Fluconazole and Voriconazole Susceptibilities of Candida Bloodstream Isolates in Korea: Use of the CLSI and EUCAST Epidemiological Cutoff Values

    PubMed Central

    Jang, Min Joong; Lee, Wee Gyo; Kim, Mi-Na; Lee, Kyungwon; Lee, Hye Soo; Lee, Mi-Kyung; Chang, Chulhun L.; Jang, Hee-Chang; Song, Eun Song; Kim, Soo Hyun; Shin, Myung-Geun; Suh, Soon-Pal; Ryang, Dong-Wook

    2013-01-01

    Background At present, the clinical breakpoints (CBPs) of both fluconazole and voriconazole are available only for 3 common Candida species in the Clinical and Laboratory Standards Institute (CLSI) and the European Committee on Antimicrobial Susceptibility Testing (EUCAST) methods. Epidemiological cutoff values (ECVs) were recently applied to both methods to detect the emergence of acquired resistance (i.e., non-wild-type isolates) among 5 common Candida species. Methods We performed a nationwide study to determine the fluconazole and voriconazole susceptibility of Candida bloodstream isolates (BSIs) using both the CLSI and EUCAST methods. A total of 423 BSIs of 5 Candida species were collected from 8 hospitals. The azole susceptibilities were assessed on the basis of the species-specific CBPs and ECVs. Results Of the 341 BSIs of 3 common Candida species (i.e., C. albicans, C. tropicalis, and C. parapsilosis), 0.3% and 0.9%, 0.0% and 1.5% of isolates were categorized as fluconazole and voriconazole resistant according to the CLSI and EUCAST CBPs, respectively. Of 423 total BSIs, 1.4% and 2.6% had fluconazole minimum inhibitory concentrations (MICs) exceeding the ECVs according to the CLSI and EUCAST, respectively; 1.0% and 2.1% had voriconazole MICs exceeding the ECVs according to the CLSI and EUCAST, respectively. Categorical agreement between the methods using ECVs was 98.3% for fluconazole and 98.3% for voriconazole. Conclusions The EUCAST and CLSI methods using ECVs provide highly concordant results. Moreover, non-wild-type isolates with possibly acquired azole resistance were rare among the BSIs of 5 common Candida species in Korea. PMID:23667842

  7. 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

  8. Racial and Ethnic Differences in the Epidemiology of Lung Cancer and the Lung Cancer Genome

    PubMed Central

    Schabath, Matthew B.; Cress, W. Douglas; Muñoz-Antonia, Teresita

    2017-01-01

    Background Globally and in the United States, lung cancer has been the most common cancer for the past several decades. In addition to the well-established geographical- and sex-specific differences in lung cancer incidence, mortality and survival, there is also growing evidence for racial and ethnic differences. Methods Based on available published data, we present a summary of the current knowledge and substantive findings related to racial and ethnic differences in lung cancer. Results Although this report is not a systematic review, we summarized the current knowledge and substantive findings related to racial and ethnic differences in lung cancer with a particular focus on lung cancer statistics(incidence, mortality, and survival), cigarette smoking, prevention and early detection, and the lung cancer genome. Finally, we summarize some the systems-level and provider-related issues that likely contribute to racial and ethnic-specific health disparities and provide some suggestions for future strategies that may reduce the disproportionate burden of lung cancer. Conclusions Although lung carcinogenesis is a multifactorial process driven by exogenous exposures (e.g., cigarette smoking), inherited genetic variations, and an accumulation of somatic genetic events, this multifactorial process appears to have racial and ethnic differences which in turn impacts the observed epidemiologic differences in incidence, mortality, and survival. PMID:27842323

  9. 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

  10. 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.

  11. Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data

    PubMed Central

    Jombart, Thibaut; Cori, Anne; Didelot, Xavier; Cauchemez, Simon; Fraser, Christophe; Ferguson, Neil

    2014-01-01

    Recent years have seen progress in the development of statistically rigorous frameworks to infer outbreak transmission trees (“who infected whom”) from epidemiological and genetic data. Making use of pathogen genome sequences in such analyses remains a challenge, however, with a variety of heuristic approaches having been explored to date. We introduce a statistical method exploiting both pathogen sequences and collection dates to unravel the dynamics of densely sampled outbreaks. Our approach identifies likely transmission events and infers dates of infections, unobserved cases and separate introductions of the disease. It also proves useful for inferring numbers of secondary infections and identifying heterogeneous infectivity and super-spreaders. After testing our approach using simulations, we illustrate the method with the analysis of the beginning of the 2003 Singaporean outbreak of Severe Acute Respiratory Syndrome (SARS), providing new insights into the early stage of this epidemic. Our approach is the first tool for disease outbreak reconstruction from genetic data widely available as free software, the R package outbreaker. It is applicable to various densely sampled epidemics, and improves previous approaches by detecting unobserved and imported cases, as well as allowing multiple introductions of the pathogen. Because of its generality, we believe this method will become a tool of choice for the analysis of densely sampled disease outbreaks, and will form a rigorous framework for subsequent methodological developments. PMID:24465202

  12. 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

  13. Full-length genomic analysis of porcine G9P[23] and G9P[7] rotavirus strains isolated from pigs with diarrhea in South Korea.

    PubMed

    Kim, Ha-Hyun; Matthijnssens, Jelle; Kim, Hyun-Jeong; Kwon, Hyung-Jun; Park, Jun-Gyu; Son, Kyu-Yeol; Ryu, Eun-Hye; Kim, Deok-Song; Lee, Woo Song; Kang, Mun-Il; Yang, Dong-Kun; Hyun, Bang-Hun; Park, Sang-Ik; Park, Su-Jin; Cho, Kyoung-Oh

    2012-10-01

    Group A rotaviruses (RVAs) are agents causing severe gastroenteritis in infants and young animals. G9 RVA strains are believed to have originated from pigs. However, this genotype has emerged as the fifth major human RVA genotype worldwide. To better understand the relationship between human and porcine RVA strains, complete RVA genome data are needed. For human RVA strains, the number of complete genome data have grown exponentially. However, there is still a lack of complete genome data on porcine RVA strains. Recently, G9 RVA strains have been identified as the third most important genotype in diarrheic pigs in South Korea in combinations with P[7] and P[23]. This study is the first report on complete genome analyses of 1 G9P[7] and 3 G9P[23] porcine RVA strains, resulting in the following genotype constellation: G9-P[7]/P[23]-I5-R1-C1-M1-A8-N1-T1-E1-H1. By comparisons of these genotype constellations, it was revealed that the Korean G9P[7] and G9P[23] RVA strains possessed a typical porcine RVA backbone, similar to other known porcine RVA strains. However, detailed phylogenetic analyses revealed the presence of intra-genotype reassortments among porcine RVA strains in South Korea. Thus, our data provide genetic information of G9 RVA strains increasingly detected in both humans and pigs, and will help to establish the role of pigs as a source or reservoir for novel human RVA strains.

  14. Deciphering the origins and tracking the evolution of cholera epidemics with whole-genome-based molecular epidemiology.

    PubMed

    Grad, Yonatan H; Waldor, Matthew K

    2013-09-10

    The devastating Haitian cholera outbreak that began in October 2010 is the first known cholera epidemic in this island nation. Epidemiological and genomic data have provided strong evidence that United Nations security forces from Nepal introduced toxigenic Vibrio cholerae O1, the cause of epidemic cholera, to Haiti shortly before the outbreak arose. However, some have contended that indigenous V. cholerae contributed to the outbreak. In a recent paper (mBio 4:e00398-13, 2013), L. S. Katz et al. explored the nature and rate of changes in this ancient pathogen's genome during an outbreak, based on whole-genome sequencing of 23 Haitian V. cholerae clinical isolates obtained over a 20-month period. Notably, they detected point mutations, deletions, and inversions but found no insertion of horizontally transmitted DNA, arguing strongly against the idea that autochthonous V. cholerae donated DNA to the outbreak strain. Furthermore, they found that Haitian epidemic V. cholerae isolates were virtually untransformable. Comparative genomic analyses revealed that the Haitian isolates were nearly identical to isolates from Nepal and that the Nepalese-Haitian isolates were distinguishable from isolates circulating elsewhere in the world. Reconstruction of the phylogeny of the Haitian isolates was consistent with a single introduction of V. cholerae to Haiti sometime between late July and late October 2010, dates remarkably concordant with epidemiological observations. In aggregate, this paper provides additional compelling evidence that the V. cholerae strain responsible for the Haitian cholera epidemic came from Nepal and illustrates the power of whole-genome-based analyses for epidemiology, pathogen evolution, and forensics.

  15. Molecular epidemiology and phylogenetic distribution of the Escherichia coli pks genomic island.

    PubMed

    Johnson, James R; Johnston, Brian; Kuskowski, Michael A; Nougayrede, Jean-Philippe; Oswald, Eric

    2008-12-01

    Epidemiological and phylogenetic associations of the pks genomic island of extraintestinal pathogenic Escherichia coli (ExPEC), which encodes the genotoxin colibactin, are incompletely defined. clbB and clbN (as markers for the 5' and 3' regions of the pks island, respectively), clbA and clbQ (as supplemental pks island markers), and 12 other putative ExPEC virulence genes were newly sought by PCR among 131 published E. coli isolates from hospitalized veterans (62 blood isolates and 69 fecal isolates). Blood and fecal isolates and clbB-positive and -negative isolates were compared for 66 newly and previously assessed traits. Among the 14 newly sought traits, clbB and clbN (colibactin polyketide synthesis system), hra (heat-resistant agglutinin), and vat (vacuolating toxin) were significantly associated with bacteremia. clbB and clbN identified a subset within phylogenetic group B2 with extremely high virulence scores and a high proportion of blood isolates. However, by multivariable analysis, other traits were more predictive of blood source than clbB and clbN were; indeed, among the newly sought traits, only pic significantly predicted bacteremia (negative association). By correspondence analysis, clbB and clbN were closely associated with group B2 and multiple B2-associated traits; by principal coordinate analysis, clbB and clbN partitioned the data set better than did blood versus fecal source. Thus, the pks island was significantly associated with bacteremia, multiple ExPEC-associated virulence genes, and group B2, and within group B2, it identified an especially high-virulence subset. This extends previous work regarding the pks island and supports investigation of the colibactin system as a potential therapeutic target.

  16. Genetic variability among complete human respiratory syncytial virus subgroup A genomes: bridging molecular evolutionary dynamics and epidemiology.

    PubMed

    Tan, Lydia; Lemey, Philippe; Houspie, Lieselot; Viveen, Marco C; Jansen, Nicolaas J G; van Loon, Anton M; Wiertz, Emmanuel; van Bleek, Grada M; Martin, Darren P; Coenjaerts, Frank E

    2012-01-01

    Human respiratory syncytial virus (RSV) is an important cause of severe lower respiratory tract infections in infants and the elderly. In the vast majority of cases, however, RSV infections run mild and symptoms resemble those of a common cold. The immunological, clinical, and epidemiological profile of severe RSV infections suggests a disease caused by a virus with typical seasonal transmission behavior, lacking clear-cut virulence factors, but instead causing disease by modifying the host's immune response in a way that stimulates pathogenesis. Yet, the interplay between RSV-evoked immune responses and epidemic behavior, and how this affects the genomic evolutionary dynamics of the virus, remains poorly understood. Here, we present a comprehensive collection of 33 novel RSV subgroup A genomes from strains sampled over the last decade, and provide the first measurement of RSV-A genomic diversity through time in a phylodynamic framework. In addition, we map amino acid substitutions per protein to determine mutational hotspots in specific domains. Using Bayesian genealogical inference, we estimated the genomic evolutionary rate to be 6.47 × 10(-4) (credible interval: 5.56 × 10(-4), 7.38 × 10(-4)) substitutions/site/year, considerably slower than previous estimates based on G gene sequences only. The G gene is however marked by elevated substitution rates compared to other RSV genes, which can be attributed to relaxed selective constraints. In line with this, site-specific selection analyses identify the G gene as the major target of diversifying selection. Importantly, statistical analysis demonstrates that the immune driven positive selection does not leave a measurable imprint on the genome phylogeny, implying that RSV lineage replacement mainly follows nonselective epidemiological processes. The roughly 50 years of RSV-A genomic evolution are characterized by a constant population size through time and general co-circulation of lineages over many epidemic

  17. 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

  18. 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.

  19. 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

  20. Plasmid Classification in an Era of Whole-Genome Sequencing: Application in Studies of Antibiotic Resistance Epidemiology

    PubMed Central

    Orlek, Alex; Stoesser, Nicole; Anjum, Muna F.; Doumith, Michel; Ellington, Matthew J.; Peto, Tim; Crook, Derrick; Woodford, Neil; Walker, A. Sarah; Phan, Hang; Sheppard, Anna E.

    2017-01-01

    Plasmids are extra-chromosomal genetic elements ubiquitous in bacteria, and commonly transmissible between host cells. Their genomes include variable repertoires of ‘accessory genes,’ such as antibiotic resistance genes, as well as ‘backbone’ loci which are largely conserved within plasmid families, and often involved in key plasmid-specific functions (e.g., replication, stable inheritance, mobility). Classifying plasmids into different types according to their phylogenetic relatedness provides insight into the epidemiology of plasmid-mediated antibiotic resistance. Current typing schemes exploit backbone loci associated with replication (replicon typing), or plasmid mobility (MOB typing). Conventional PCR-based methods for plasmid typing remain widely used. With the emergence of whole-genome sequencing (WGS), large datasets can be analyzed using in silico plasmid typing methods. However, short reads from popular high-throughput sequencers can be challenging to assemble, so complete plasmid sequences may not be accurately reconstructed. Therefore, localizing resistance genes to specific plasmids may be difficult, limiting epidemiological insight. Long-read sequencing will become increasingly popular as costs decline, especially when resolving accurate plasmid structures is the primary goal. This review discusses the application of plasmid classification in WGS-based studies of antibiotic resistance epidemiology; novel in silico plasmid analysis tools are highlighted. Due to the diverse and plastic nature of plasmid genomes, current typing schemes do not classify all plasmids, and identifying conserved, phylogenetically concordant genes for subtyping and phylogenetics is challenging. Analyzing plasmids as nodes in a network that represents gene-sharing relationships between plasmids provides a complementary way to assess plasmid diversity, and allows inferences about horizontal gene transfer to be made. PMID:28232822

  1. Plasmid Classification in an Era of Whole-Genome Sequencing: Application in Studies of Antibiotic Resistance Epidemiology.

    PubMed

    Orlek, Alex; Stoesser, Nicole; Anjum, Muna F; Doumith, Michel; Ellington, Matthew J; Peto, Tim; Crook, Derrick; Woodford, Neil; Walker, A Sarah; Phan, Hang; Sheppard, Anna E

    2017-01-01

    Plasmids are extra-chromosomal genetic elements ubiquitous in bacteria, and commonly transmissible between host cells. Their genomes include variable repertoires of 'accessory genes,' such as antibiotic resistance genes, as well as 'backbone' loci which are largely conserved within plasmid families, and often involved in key plasmid-specific functions (e.g., replication, stable inheritance, mobility). Classifying plasmids into different types according to their phylogenetic relatedness provides insight into the epidemiology of plasmid-mediated antibiotic resistance. Current typing schemes exploit backbone loci associated with replication (replicon typing), or plasmid mobility (MOB typing). Conventional PCR-based methods for plasmid typing remain widely used. With the emergence of whole-genome sequencing (WGS), large datasets can be analyzed using in silico plasmid typing methods. However, short reads from popular high-throughput sequencers can be challenging to assemble, so complete plasmid sequences may not be accurately reconstructed. Therefore, localizing resistance genes to specific plasmids may be difficult, limiting epidemiological insight. Long-read sequencing will become increasingly popular as costs decline, especially when resolving accurate plasmid structures is the primary goal. This review discusses the application of plasmid classification in WGS-based studies of antibiotic resistance epidemiology; novel in silico plasmid analysis tools are highlighted. Due to the diverse and plastic nature of plasmid genomes, current typing schemes do not classify all plasmids, and identifying conserved, phylogenetically concordant genes for subtyping and phylogenetics is challenging. Analyzing plasmids as nodes in a network that represents gene-sharing relationships between plasmids provides a complementary way to assess plasmid diversity, and allows inferences about horizontal gene transfer to be made.

  2. Complete genome sequences of three tomato spotted wilt virus isolates from tomato and pepper plants in Korea and their phylogenetic relationship to other TSWV isolates.

    PubMed

    Lee, Jong-Seung; Cho, Won Kyong; Kim, Mi-Kyeong; Kwak, Hae-Ryun; Choi, Hong-Soo; Kim, Kook-Hyung

    2011-04-01

    Tomato spotted wilt virus (TSWV) infects numerous host plants and has three genome segments, called L, M and S. Here, we report the complete genome sequences of three Korean TSWV isolates (TSWV-1 to -3) infecting tomato and pepper plants. Although the nucleotide sequence of TSWV-1 genome isolated from tomato is very different from those of TSWV-2 and TSWV-3 isolated from pepper, the deduced amino acid sequences of the five TSWV genes are highly conserved among all three TSWV isolates. In phylogenetic analysis, deduced RdRp protein sequences of TSWV-2 and TSWV-3 were clustered together with two previously reported isolates from Japan and Korea, while TSWV-1 grouped together with a Hawaiian isolate. A phylogenetic tree based on N protein sequences, however, revealed four distinct groups of TSWV isolates, and all three Korean isolates belonged to group II, together with many other isolates, mostly from Europe and Asia. Interestingly, most American isolates grouped together as group I. Together, these results suggested that these newly identified TSWV isolates might have originated from an Asian ancestor and undergone divergence upon infecting different host plants.

  3. 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

  4. [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

  5. Genomic epidemiology of the Haitian cholera outbreak: a single introduction followed by rapid, extensive, and continued spread characterized the onset of the epidemic.

    PubMed

    Eppinger, Mark; Pearson, Talima; Koenig, Sara S K; Pearson, Ofori; Hicks, Nathan; Agrawal, Sonia; Sanjar, Fatemeh; Galens, Kevin; Daugherty, Sean; Crabtree, Jonathan; Hendriksen, Rene S; Price, Lance B; Upadhyay, Bishnu P; Shakya, Geeta; Fraser, Claire M; Ravel, Jacques; Keim, Paul S

    2014-11-04

    For centuries, cholera has been one of the most feared diseases. The causative agent Vibrio cholerae is a waterborne Gram-negative enteric pathogen eliciting a severe watery diarrheal disease. In October 2010, the seventh pandemic reached Haiti, a country that had not experienced cholera for more than a century. By using whole-genome sequence typing and mapping strategies of 116 serotype O1 strains from global sources, including 44 Haitian genomes, we present a detailed reconstructed evolutionary history of the seventh pandemic with a focus on the Haitian outbreak. We catalogued subtle genomic alterations at the nucleotide level in the genome core and architectural rearrangements from whole-genome map comparisons. Isolates closely related to the Haitian isolates caused several recent outbreaks in southern Asia. This study provides evidence for a single-source introduction of cholera from Nepal into Haiti followed by rapid, extensive, and continued clonal expansion. The phylogeographic patterns in both southern Asia and Haiti argue for the rapid dissemination of V. cholerae across the landscape necessitating real-time surveillance efforts to complement the whole-genome epidemiological analysis. As eradication efforts move forward, phylogeographic knowledge will be important for identifying persistent sources and monitoring success at regional levels. The results of molecular and epidemiological analyses of this outbreak suggest that an indigenous Haitian source of V. cholerae is unlikely and that an indigenous source has not contributed to the genomic evolution of this clade. In this genomic epidemiology study, we have applied high-resolution whole-genome-based sequence typing methodologies on a comprehensive set of genome sequences that have become available in the aftermath of the Haitian cholera epidemic. These sequence resources enabled us to reassess the degree of genomic heterogeneity within the Vibrio cholerae O1 serotype and to refine boundaries and

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

    PubMed Central

    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

    2016-01-01

    The emergence of Neisseria gonorrhoeae strains with decreased susceptibility to cephalosporins and azithromycin (AZM) resistance (AZMr) represents a public health threat of untreatable gonorrhea infections. Genomic epidemiology through whole-genome sequencing was used to describe the emergence, dissemination, and spread of AZMr strains. The genomes of 213 AZMr and 23 AZM-susceptible N. gonorrhoeae isolates collected in Canada from 1989 to 2014 were sequenced. Core single nucleotide polymorphism (SNP) phylogenomic analysis resolved 246 isolates into 13 lineages. High-level AZMr (MICs ≥ 256 μg/ml) was found in 5 phylogenetically diverse isolates, all of which possessed the A2059G mutation (Escherichia coli numbering) in all four 23S rRNA alleles. One isolate with high-level AZMr collected in 2009 concurrently had decreased susceptibility to ceftriaxone (MIC = 0.125 μg/ml). An increase in the number of 23S rRNA alleles with the C2611T mutations (E. coli numbering) conferred low to moderate levels of AZMr (MICs = 2 to 4 and 8 to 32 μg/ml, respectively). Low-level AZMr was also associated with mtrR promoter mutations, including the −35A deletion and the presence of Neisseria meningitidis-like sequences. Geographic and temporal phylogenetic clustering indicates that emergent AZMr strains arise independently and can then rapidly expand clonally in a region through local sexual networks. PMID:26935729

  7. Molecular epidemiology of Crimean- Congo hemorrhagic fever virus genome isolated from ticks of Hamadan province of Iran.

    PubMed

    Tahmasebi, F; Ghiasi, S M; Mostafavi, E; Moradi, M; Piazak, N; Mozafari, A; Haeri, A; Fooks, A R; Chinikar, S

    2010-12-01

    Crimean-Congo hemorrhagic fever (CCHF) virus is a tick-borne member of the genus Nairovirus, family Bunyaviridae. CCHFV has been isolated from at least 31 different tick species. The virus is transmitted through the bite of an infected tick, or by direct contact with CCHFV-infected patients or the products of infected livestock. This study was undertaken to study the genetic relationship and distribution of CCHFV in the tick population of Hamadan province of Iran. In this study, RT-PCR has been used for detection of the CCHFV genome. This genome was detected in 19.2% of the ticks collected from livestock of different regions of the Hamadan province in western Iran. The infected species belonged to Hyalomma detritum, H. anatolicum, Rhipicephalus sanguineus and Argas reflexus. With one exception, genetic analysis of the virus genome isolates showed high sequence identity to each other. Even though they clustered in the same group with the strain circulating in Iran, they had a closer relationship to the Matin strain. Vector control programs should be applied for reducing population density of potential tick vectors in this province. Further surveys are indicated in this region to provide a better view of the distribution and epidemiology of the virus.

  8. Genome-wide studies of verbal declarative memory in nondemented older people: the Cohorts for Heart and Aging Research in Genomic Epidemiology consortium.

    PubMed

    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, M Arfan; Deary, Ian J; van Duijn, Cornelia M; Launer, Lenore; Fitzpatrick, Annette L; Seshadri, Sudha; Mosley, Thomas H

    2015-04-15

    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. 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. 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. 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. Copyright © 2015 Society of Biological Psychiatry. Published by Elsevier Inc. All rights reserved.

  9. 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

  10. Genomic epidemiology of Lineage 4 Mycobacterium tuberculosis subpopulations in New York City and New Jersey, 1999-2009.

    PubMed

    Brown, Tyler S; Narechania, Apurva; Walker, John R; Planet, Paul J; Bifani, Pablo J; Kolokotronis, Sergios-Orestis; Kreiswirth, Barry N; Mathema, Barun

    2016-11-21

    Whole genome sequencing (WGS) has rapidly become an important research tool in tuberculosis epidemiology and is likely to replace many existing methods in public health microbiology in the near future. WGS-based methods may be particularly useful in areas with less diverse Mycobacterium tuberculosis populations, such as New York City, where conventional genotyping is often uninformative and field epidemiology often difficult. This study applies four candidate strategies for WGS-based identification of emerging M. tuberculosis subpopulations, employing both phylogenomic and population genetics methods. M. tuberculosis subpopulations in New York City and New Jersey can be distinguished via phylogenomic reconstruction, evidence of demographic expansion and subpopulation-specific signatures of selection, and by determination of subgroup-defining nucleotide substitutions. These methods identified known historical outbreak clusters and previously unidentified subpopulations within relatively monomorphic M. tuberculosis endemic clone groups. Neutrality statistics based on the site frequency spectrum were less useful for identifying M. tuberculosis subpopulations, likely due to the low levels of informative genetic variation in recently diverged isolate groups. In addition, we observed that isolates from New York City endemic clone groups have acquired multiple non-synonymous SNPs in virulence- and growth-associated pathways, and relatively few mutations in drug resistance-associated genes, suggesting that overall pathoadaptive fitness, rather than the acquisition of drug resistance mutations, has played a central role in the evolutionary history and epidemiology of M. tuberculosis subpopulations in New York City. Our results demonstrate that some but not all WGS-based methods are useful for detection of emerging M. tuberculosis clone groups, and support the use of phylogenomic reconstruction in routine tuberculosis laboratory surveillance, particularly in areas with

  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. 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

  13. Molecular epidemiology of bovine rotaviruses. Characterization of rotaviruses isolated from diarrhoeic calves by genome profile analysis.

    PubMed

    Legrottaglie, R; Rizzi, V; Agrimi, P

    1995-04-01

    Fifteen bovine rotavirus group A strains were isolated in several Italian regions over the period 1981-1989 from calves in ten neonatal diarrhoea outbreaks. The electrophoretical analysis of the genoma showed genomic variations and five different profiles were observed, including one with thirteen dsRNA segments. The finding of extra RNA fragments, with respect to the regular eleven genome segments, suggests the possibility of simultaneous or sequential infection by more than one electropherotype or a modification in the length of RNA segments during infection.

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

    USDA-ARS?s Scientific Manuscript database

    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...

  15. Genomic and Epidemiological Evidence for Community Origins of Hospital-Onset Methicillin-Resistant Staphylococcus aureus Bloodstream Infections.

    PubMed

    Popovich, Kyle J; Snitkin, Evan S; Hota, Bala; Green, Stefan J; Pirani, Ali; Aroutcheva, Alla; Weinstein, Robert A

    2017-06-01

    We examined whether disparities existed in hospital-onset (HO) Staphylococcus aureus bloodstream infections (BSIs) and used whole-genome sequencing (WGS) to identify factors associated with USA300 transmission networks. We evaluated HO methicillin-susceptible S. aureus (MSSA) and HO methicillin-resistant S. aureus (MRSA) BSIs for 2009-2013 at 2 hospitals and used an adjusted incidence for modeling. WGS and phylogenetic analyses were performed on a sample of USA300 BSI isolates. Epidemiologic data were analyzed in the context of phylogenetic reconstructions. On multivariate analysis, male sex, African-American race, and non-Hispanic white race/ethnicity were significantly associated with HO-MRSA BSIs whereas Hispanic ethnicity was negatively associated (rate ratio, 0.41; P = .002). Intermixing of community-onset and HO-USA300 strains on the phylogenetic tree indicates that these strains derive from a common pool. African-American race was the only factor associated with genomic clustering of isolates. In a multicenter assessment of HO-S. aureus BSIs, African-American race was significantly associated with HO-MRSA but not MSSA BSIs. There appears to be a nexus of USA300 community and hospital transmission networks, with a community factor being the primary driver. Our data suggest that HO-USA300 BSIs likely are due to colonizing strains acquired in the community before hospitalization. Therefore, prevention efforts may need to extend to the community for maximal benefit.

  16. 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

  17. Genomic Epidemiology of the Haitian Cholera Outbreak: a Single Introduction Followed by Rapid, Extensive, and Continued Spread Characterized the Onset of the Epidemic

    PubMed Central

    Pearson, Talima; Koenig, Sara S. K.; Pearson, Ofori; Hicks, Nathan; Agrawal, Sonia; Sanjar, Fatemeh; Galens, Kevin; Daugherty, Sean; Crabtree, Jonathan; Hendriksen, Rene S.; Price, Lance B.; Upadhyay, Bishnu P.; Shakya, Geeta; Fraser, Claire M.; Ravel, Jacques

    2014-01-01

    ABSTRACT For centuries, cholera has been one of the most feared diseases. The causative agent Vibrio cholerae is a waterborne Gram-negative enteric pathogen eliciting a severe watery diarrheal disease. In October 2010, the seventh pandemic reached Haiti, a country that had not experienced cholera for more than a century. By using whole-genome sequence typing and mapping strategies of 116 serotype O1 strains from global sources, including 44 Haitian genomes, we present a detailed reconstructed evolutionary history of the seventh pandemic with a focus on the Haitian outbreak. We catalogued subtle genomic alterations at the nucleotide level in the genome core and architectural rearrangements from whole-genome map comparisons. Isolates closely related to the Haitian isolates caused several recent outbreaks in southern Asia. This study provides evidence for a single-source introduction of cholera from Nepal into Haiti followed by rapid, extensive, and continued clonal expansion. The phylogeographic patterns in both southern Asia and Haiti argue for the rapid dissemination of V. cholerae across the landscape necessitating real-time surveillance efforts to complement the whole-genome epidemiological analysis. As eradication efforts move forward, phylogeographic knowledge will be important for identifying persistent sources and monitoring success at regional levels. The results of molecular and epidemiological analyses of this outbreak suggest that an indigenous Haitian source of V. cholerae is unlikely and that an indigenous source has not contributed to the genomic evolution of this clade. PMID:25370488

  18. Full-Genomic Analysis of a Human Norovirus Recombinant GII.12/13 Novel Strain Isolated from South Korea

    PubMed Central

    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. PMID:24391985

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

    PubMed Central

    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. PMID

  20. 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.

  1. 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

  2. Functional variants of human papillomavirus type 16 demonstrate host genome integration and transcriptional alterations corresponding to their unique cancer epidemiology.

    PubMed

    Jackson, Robert; Rosa, Bruce A; Lameiras, Sonia; Cuninghame, Sean; Bernard, Josee; Floriano, Wely B; Lambert, Paul F; Nicolas, Alain; Zehbe, Ingeborg

    2016-11-02

    Human papillomaviruses (HPVs) are a worldwide burden as they are a widespread group of tumour viruses in humans. Having a tropism for mucosal tissues, high-risk HPVs are detected in nearly all cervical cancers. HPV16 is the most common high-risk type but not all women infected with high-risk HPV develop a malignant tumour. Likely relevant, HPV genomes are polymorphic and some HPV16 single nucleotide polymorphisms (SNPs) are under evolutionary constraint instigating variable oncogenicity and immunogenicity in the infected host. To investigate the tumourigenicity of two common HPV16 variants, we used our recently developed, three-dimensional organotypic model reminiscent of the natural HPV infectious cycle and conducted various "omics" and bioinformatics approaches. Based on epidemiological studies we chose to examine the HPV16 Asian-American (AA) and HPV16 European Prototype (EP) variants. They differ by three non-synonymous SNPs in the transforming and virus-encoded E6 oncogene where AAE6 is classified as a high- and EPE6 as a low-risk variant. Remarkably, the high-risk AAE6 variant genome integrated into the host DNA, while the low-risk EPE6 variant genome remained episomal as evidenced by highly sensitive Capt-HPV sequencing. RNA-seq experiments showed that the truncated form of AAE6, integrated in chromosome 5q32, produced a local gene over-expression and a large variety of viral-human fusion transcripts, including long distance spliced transcripts. In addition, differential enrichment of host cell pathways was observed between both HPV16 E6 variant-containing epithelia. Finally, in the high-risk variant, we detected a molecular signature of host chromosomal instability, a common property of cancer cells. We show how naturally occurring SNPs in the HPV16 E6 oncogene cause significant changes in the outcome of HPV infections and subsequent viral and host transcriptome alterations prone to drive carcinogenesis. Host genome instability is closely linked to viral

  3. Genomic epidemiology of Vibrio cholerae O1 associated with floods, Pakistan, 2010.

    PubMed

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

    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.

  4. 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

  5. Evolution, genomics and epidemiology of Pseudomonas syringae: Challenges in Bacterial Molecular Plant Pathology.

    PubMed

    Baltrus, David A; McCann, Honour C; Guttman, David S

    2017-01-01

    A remarkable shift in our understanding of plant-pathogenic bacteria is underway. Until recently, nearly all research on phytopathogenic bacteria was focused on a small number of model strains, which provided a deep, but narrow, perspective on plant-microbe interactions. Advances in genome sequencing technologies have changed this by enabling the incorporation of much greater diversity into comparative and functional research. We are now moving beyond a typological understanding of a select collection of strains to a more generalized appreciation of the breadth and scope of plant-microbe interactions. The study of natural populations and evolution has particularly benefited from the expansion of genomic data. We are beginning to have a much deeper understanding of the natural genetic diversity, niche breadth, ecological constraints and defining characteristics of phytopathogenic species. Given this expanding genomic and ecological knowledge, we believe the time is ripe to evaluate what we know about the evolutionary dynamics of plant pathogens. © 2016 BSPP and John Wiley & Sons Ltd.

  6. Complete genome sequence of canine astrovirus with molecular and epidemiological characterisation of UK strains.

    PubMed

    Caddy, Sarah L; Goodfellow, Ian

    2015-05-15

    Astroviruses are a common cause of gastroenteritis in children worldwide. These viruses can also cause infection in a range of domestic and wild animal species. Canine astrovirus (CaAstV) was first identified in the USA, and has since been reported in dogs from Europe, the Far East and South America. We sought to determine whether CaAstV is circulating in the UK dog population, and to characterise any identified strains. Stool samples were collected from pet dogs in the UK with and without gastroenteritis, and samples were screened for CaAstV by qPCR. Four CaAstV positive samples were identified from dogs with gastroenteritis (4/67, 6.0%), whereas no samples from healthy dogs were positive (p<0.001). Sequencing of the capsid sequences from the four CaAstV strains found significant genetic heterogeneity, with only 80% amino acid identity between strains. The full genome sequence of two UK CaAstV strains was then determined, confirming that CaAstV conforms to the classic genome organisation of other astroviruses with ORF1a and ORF1b separated by a frameshift and ORF2 encoding the capsid protein. This is the first report describing the circulation of CaAstV in UK dogs with clinical signs of gastroenteritis, and the first description of the full-length genomes of two CaAstV strains.

  7. Epidemeology and Serology of Typhoid Fever Including Survey on Salmonella in Korea.

    DTIC Science & Technology

    EPIDEMIOLOGY, *TYPHOID, SENSITIVITY, MEDIA, PUBLIC HEALTH, CULTURES(BIOLOGY), SOUTH KOREA, SHIGELLA, ANTIBIOTICS , RESISTANCE (BIOLOGY), BLOOD ANALYSIS, FOOD HANDLERS, SALMONELLA PARATYPHI, SALMONELLA TYPHIMURIUM.

  8. 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

  9. Genome-Wide Gene-Sodium Interaction Analyses on Blood Pressure: The Genetic Epidemiology Network of Salt-Sensitivity Study.

    PubMed

    Li, Changwei; He, Jiang; Chen, Jing; Zhao, Jinying; Gu, Dongfeng; Hixson, James E; Rao, Dabeeru C; Jaquish, Cashell E; Gu, Charles C; Chen, Jichun; Huang, Jianfeng; Chen, Shufeng; Kelly, Tanika N

    2016-08-01

    We performed genome-wide analyses to identify genomic loci that interact with sodium to influence blood pressure (BP) using single-marker-based (1 and 2 df joint tests) and gene-based tests among 1876 Chinese participants of the Genetic Epidemiology Network of Salt-Sensitivity (GenSalt) study. Among GenSalt participants, the average of 3 urine samples was used to estimate sodium excretion. Nine BP measurements were taken using a random zero sphygmomanometer. A total of 2.05 million single-nucleotide polymorphisms were imputed using Affymetrix 6.0 genotype data and the Chinese Han of Beijing and Japanese of Tokyo HapMap reference panel. Promising findings (P<1.00×10(-4)) from GenSalt were evaluated for replication among 775 Chinese participants of the Multi-Ethnic Study of Atherosclerosis (MESA). Single-nucleotide polymorphism and gene-based results were meta-analyzed across the GenSalt and MESA studies to determine genome-wide significance. The 1 df tests identified interactions for UST rs13211840 on diastolic BP (P=3.13×10(-9)). The 2 df tests additionally identified associations for CLGN rs2567241 (P=3.90×10(-12)) and LOC105369882 rs11104632 (P=4.51×10(-8)) with systolic BP. The CLGN variant rs2567241 was also associated with diastolic BP (P=3.11×10(-22)) and mean arterial pressure (P=2.86×10(-15)). Genome-wide gene-based analysis identified MKNK1 (P=6.70×10(-7)), C2orf80 (P<1.00×10(-12)), EPHA6 (P=2.88×10(-7)), SCOC-AS1 (P=4.35×10(-14)), SCOC (P=6.46×10(-11)), CLGN (P=3.68×10(-13)), MGAT4D (P=4.73×10(-11)), ARHGAP42 (P≤1.00×10(-12)), CASP4 (P=1.31×10(-8)), and LINC01478 (P=6.75×10(-10)) that were associated with at least 1 BP phenotype. In summary, we identified 8 novel and 1 previously reported BP loci through the examination of single-nucleotide polymorphism and gene-based interactions with sodium.

  10. Genomic epidemiology of global Klebsiella pneumoniae carbapenemase (KPC)-producing Escherichia coli.

    PubMed

    Stoesser, N; Sheppard, A E; Peirano, G; Anson, L W; Pankhurst, L; Sebra, R; Phan, H T T; Kasarskis, A; Mathers, A J; Peto, T E A; Bradford, P; Motyl, M R; Walker, A S; Crook, D W; Pitout, J D

    2017-07-19

    The dissemination of carbapenem resistance in Escherichia coli has major implications for the management of common infections. bla KPC, encoding a transmissible carbapenemase (KPC), has historically largely been associated with Klebsiella pneumoniae, a predominant plasmid (pKpQIL), and a specific transposable element (Tn4401, ~10 kb). Here we characterize the genetic features of bla KPC emergence in global E. coli, 2008-2013, using both long- and short-read whole-genome sequencing. Amongst 43/45 successfully sequenced bla KPC-E. coli strains, we identified substantial strain diversity (n = 21 sequence types, 18% of annotated genes in the core genome); substantial plasmid diversity (≥9 replicon types); and substantial bla KPC-associated, mobile genetic element (MGE) diversity (50% not within complete Tn4401 elements). We also found evidence of inter-species, regional and international plasmid spread. In several cases bla KPC was found on high copy number, small Col-like plasmids, previously associated with horizontal transmission of resistance genes in the absence of antimicrobial selection pressures. E. coli is a common human pathogen, but also a commensal in multiple environmental and animal reservoirs, and easily transmissible. The association of bla KPC with a range of MGEs previously linked to the successful spread of widely endemic resistance mechanisms (e.g. bla TEM, bla CTX-M) suggests that it may become similarly prevalent.

  11. The impact of indiscriminate media coverage of a celebrity suicide on a society with a high suicide rate: epidemiological findings on copycat suicides from South Korea.

    PubMed

    Ju Ji, Nam; Young Lee, Weon; Seok Noh, Maeng; Yip, Paul S F

    2014-03-01

    This study examines the extent to which the indiscriminate media coverage of the famous young actress Lee Eun-ju's suicide in 2005 affected suicides overall and in specific subgroups (by age, gender, and suicide method) in a suicide-prone society, South Korea. South Korea's 2003-2005 suicide data (n=34,237) were obtained from death certificate records of the National Statistical Office (NSO). Data was analyzed with Poisson time series auto-regression models. After adjusting for confounding factors (such as seasonal variation, calendar year, temperature, humidity, and unemployment rate), there was a significant increase in suicide (RR=1.40, 95%, CI=1.30-1.51, no. of excess mortalities=331; 95% CI=267-391) during the 4 weeks after Lee's suicide. This increase was more prominent in subgroups with similar characteristics to the celebrity. In particular, the relative risk of suicide during this period was the largest (5.24; 95% CI=3.31-8.29) in young women who used the same suicide method as the celebrity. Moreover, the incidence of these copycat suicides during the same time significantly increased in both genders and in all age subgroups among those who committed suicide using the same method as the celebrity (hanging). It is difficult to prove conclusively that the real motivation of the suicides was Lee's death. The findings from this study imply that, if the media indiscreetly reports the suicide of a celebrity in a suicide-prone society, the copycat effect can be far-reaching and very strong, particularly for vulnerable people. © 2013 Published by Elsevier B.V.

  12. Feral swine brucellosis in the United States and prospective genomic techniques for disease epidemiology.

    PubMed

    Leiser, Owen P; Corn, Joseph L; Schmit, Brandon S; Keim, Paul S; Foster, Jeffrey T

    2013-09-27

    Brucellosis is a common infection of feral swine throughout the United States. With the recent expansion of feral swine populations across the country, this disease poses an increasing threat to agriculture and hunters. The standard approach to Brucella surveillance in feral swine has been serological testing, which gives an indication of past exposure and is a rapid method of determining populations where Brucella is present. More in-depth analyses require bacterial isolation to determine the Brucella species and biovar involved. Ultimately, for a comprehensive understanding of Brucella epizootiology in feral swine, incorporation of genotyping assays has become essential. Fortunately, the past decade has given rise to an array of genetic tools for assessing Brucella transmission and dispersal. This review aims to synthesize what is known about brucellosis in feral swine and will cover prospective genomic techniques that may be utilized to develop more complete understanding of the disease and its transmission history. Copyright © 2013 Elsevier B.V. All rights reserved.

  13. Bacterial Genomics Reveal the Complex Epidemiology of an Emerging Pathogen in Arctic and Boreal Ungulates

    PubMed Central

    Forde, Taya L.; Orsel, Karin; Zadoks, Ruth N.; Biek, Roman; Adams, Layne G.; Checkley, Sylvia L.; Davison, Tracy; De Buck, Jeroen; Dumond, Mathieu; Elkin, Brett T.; Finnegan, Laura; Macbeth, Bryan J.; Nelson, Cait; Niptanatiak, Amanda; Sather, Shane; Schwantje, Helen M.; van der Meer, Frank; Kutz, Susan J.

    2016-01-01

    Northern ecosystems are currently experiencing unprecedented ecological change, largely driven by a rapidly changing climate. Pathogen range expansion, and emergence and altered patterns of infectious disease, are increasingly reported in wildlife at high latitudes. Understanding the causes and consequences of shifting pathogen diversity and host-pathogen interactions in these ecosystems is important for wildlife conservation, and for indigenous populations that depend on wildlife. Among the key questions are whether disease events are associated with endemic or recently introduced pathogens, and whether emerging strains are spreading throughout the region. In this study, we used a phylogenomic approach to address these questions of pathogen endemicity and spread for Erysipelothrix rhusiopathiae, an opportunistic multi-host bacterial pathogen associated with recent mortalities in arctic and boreal ungulate populations in North America. We isolated E. rhusiopathiae from carcasses associated with large-scale die-offs of muskoxen in the Canadian Arctic Archipelago, and from contemporaneous mortality events and/or population declines among muskoxen in northwestern Alaska and caribou and moose in western Canada. Bacterial genomic diversity differed markedly among these locations; minimal divergence was present among isolates from muskoxen in the Canadian Arctic, while in caribou and moose populations, strains from highly divergent clades were isolated from the same location, or even from within a single carcass. These results indicate that mortalities among northern ungulates are not associated with a single emerging strain of E. rhusiopathiae, and that alternate hypotheses need to be explored. Our study illustrates the value and limitations of bacterial genomic data for discriminating between ecological hypotheses of disease emergence, and highlights the importance of studying emerging pathogens within the broader context of environmental and host factors. PMID

  14. Bacterial Genomics Reveal the Complex Epidemiology of an Emerging Pathogen in Arctic and Boreal Ungulates.

    PubMed

    Forde, Taya L; Orsel, Karin; Zadoks, Ruth N; Biek, Roman; Adams, Layne G; Checkley, Sylvia L; Davison, Tracy; De Buck, Jeroen; Dumond, Mathieu; Elkin, Brett T; Finnegan, Laura; Macbeth, Bryan J; Nelson, Cait; Niptanatiak, Amanda; Sather, Shane; Schwantje, Helen M; van der Meer, Frank; Kutz, Susan J

    2016-01-01

    Northern ecosystems are currently experiencing unprecedented ecological change, largely driven by a rapidly changing climate. Pathogen range expansion, and emergence and altered patterns of infectious disease, are increasingly reported in wildlife at high latitudes. Understanding the causes and consequences of shifting pathogen diversity and host-pathogen interactions in these ecosystems is important for wildlife conservation, and for indigenous populations that depend on wildlife. Among the key questions are whether disease events are associated with endemic or recently introduced pathogens, and whether emerging strains are spreading throughout the region. In this study, we used a phylogenomic approach to address these questions of pathogen endemicity and spread for Erysipelothrix rhusiopathiae, an opportunistic multi-host bacterial pathogen associated with recent mortalities in arctic and boreal ungulate populations in North America. We isolated E. rhusiopathiae from carcasses associated with large-scale die-offs of muskoxen in the Canadian Arctic Archipelago, and from contemporaneous mortality events and/or population declines among muskoxen in northwestern Alaska and caribou and moose in western Canada. Bacterial genomic diversity differed markedly among these locations; minimal divergence was present among isolates from muskoxen in the Canadian Arctic, while in caribou and moose populations, strains from highly divergent clades were isolated from the same location, or even from within a single carcass. These results indicate that mortalities among northern ungulates are not associated with a single emerging strain of E. rhusiopathiae, and that alternate hypotheses need to be explored. Our study illustrates the value and limitations of bacterial genomic data for discriminating between ecological hypotheses of disease emergence, and highlights the importance of studying emerging pathogens within the broader context of environmental and host factors.

  15. Bacterial genomics reveal the complex epidemiology of an emerging pathogen in arctic and boreal ungulates

    USGS Publications Warehouse

    Forde, Taya L.; Orsel, Karin; Zadoks, Ruth N.; Biek, Roman; Adams, Layne G.; Checkley, Sylvia L.; Davison, Tracy; De Buck, Jeroen; Dumond, Mathieu; Elkin, Brett T.; Finnegan, Laura; Macbeth, Bryan J.; Nelson, Cait; Niptanatiak, Amanda; Sather, Shane; Schwantje, Helen M.; van der Meer, Frank; Kutz, Susan J.

    2016-01-01

    Northern ecosystems are currently experiencing unprecedented ecological change, largely driven by a rapidly changing climate. Pathogen range expansion, and emergence and altered patterns of infectious disease, are increasingly reported in wildlife at high latitudes. Understanding the causes and consequences of shifting pathogen diversity and host-pathogen interactions in these ecosystems is important for wildlife conservation, and for indigenous populations that depend on wildlife. Among the key questions are whether disease events are associated with endemic or recently introduced pathogens, and whether emerging strains are spreading throughout the region. In this study, we used a phylogenomic approach to address these questions of pathogen endemicity and spread for Erysipelothrix rhusiopathiae, an opportunistic multi-host bacterial pathogen associated with recent mortalities in arctic and boreal ungulate populations in North America. We isolated E. rhusiopathiae from carcasses associated with large-scale die-offs of muskoxen in the Canadian Arctic Archipelago, and from contemporaneous mortality events and/or population declines among muskoxen in northwestern Alaska and caribou and moose in western Canada. Bacterial genomic diversity differed markedly among these locations; minimal divergence was present among isolates from muskoxen in the Canadian Arctic, while in caribou and moose populations, strains from highly divergent clades were isolated from the same location, or even from within a single carcass. These results indicate that mortalities among northern ungulates are not associated with a single emerging strain of E. rhusiopathiae, and that alternate hypotheses need to be explored. Our study illustrates the value and limitations of bacterial genomic data for discriminating between ecological hypotheses of disease emergence, and highlights the importance of studying emerging pathogens within the broader context of environmental and host factors.

  16. 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

  17. Genomic Epidemiology of Penicillin-Nonsusceptible Pneumococci with Nonvaccine Serotypes Causing Invasive Disease in the United States.

    PubMed

    Andam, Cheryl P; Mitchell, Patrick K; Callendrello, Alanna; Chang, Qiuzhi; Corander, Jukka; Chaguza, Chrispin; McGee, Lesley; Beall, Bernard W; Hanage, William P

    2017-04-01

    Conjugate vaccination against seven pneumococcal serotypes (PCV7) reduced disease prevalence due to antibiotic-resistant strains throughout the 2000s. However, diseases caused by resistant nonvaccine type (NVT) strains increased. Some of these emerging strains were derived from vaccine types (VT) that had changed their capsule by recombination. The introduction of a vaccine targeting 13 serotypes (PCV13) in 2010 has led to concern that this scenario will repeat itself. We generated high-quality draft genomes from 265 isolates of NVT pneumococci not susceptible to penicillin (PNSP) in 2009 and compared them with the genomes of 581 isolates from 2012 to 2013 collected by the Active Bacterial Core surveillance (ABCs) of the Centers for Disease Control and Prevention (CDC). Of the seven sequence clusters (SCs) identified, three SCs fell into a single lineage associated with serogroup 23, which had an origin in 1908 as dated by coalescent analysis and included isolates with a divergent 23B capsule locus. Three other SCs represented relatively deep-branching lineages associated with serotypes 35B, 15A, and 15BC. In all cases, the resistant clones originated prior to 2010, indicating that PNSP are at present dominated by descendants of NVT clones present before vaccination. With one exception (15BC/ST3280), these SCs were related to clones identified by the Pneumococcal Molecular Epidemiology Network (PMEN). We conclude that postvaccine diversity in NVT PNSP between 2009 and 2013 was driven mainly by the persistence of preexisting strains rather than through de novo adaptation, with few cases of serotype switching. Future surveillance is essential for documenting the long-term dynamics and resistance of NVT PNSP.

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

    PubMed

    Fesinmeyer, Megan D; North, Kari E; Lim, Unhee; Bůžková, Petra; Crawford, Dana C; Haessler, Jeffrey; Gross, Myron D; Fowke, Jay H; Goodloe, Robert; Love, Shelley-Ann; Graff, Misa; Carlson, Christopher S; Kuller, Lewis H; Matise, Tara C; Hong, Ching-Ping; Henderson, Brian E; Allen, Melissa; Rohde, Rebecca R; Mayo, Ping; Schnetz-Boutaud, Nathalie; Monroe, Kristine R; Ritchie, Marylyn D; Prentice, Ross L; Kolonel, Lawrence N; Manson, JoAnn E; Pankow, James; Hindorff, Lucia A; Franceschini, Nora; Wilkens, Lynne R; Haiman, Christopher A; Le Marchand, Loic; Peters, Ulrike

    2013-01-11

    Although smoking behavior is known to affect body mass index (BMI), the potential for smoking to influence genetic associations with BMI is largely unexplored. 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. 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, p(interaction) = 0.10). For rs9939609/FTO, the A allele was more strongly associated with BMI among current smoker EA females (β = 0.017, p = 3.5 x 10(-5)), vs. former/never smokers (β = 0.006, p = 0.05, p(interaction) = 0.08). 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. NCT00000611.

  19. Association of Cancer Susceptibility Variants with Risk of Multiple Primary Cancers: the Population Architecture using Genomics and Epidemiology Study

    PubMed Central

    Park, S. Lani; Caberto, Christian P.; Lin, Yi; Goodloe, Robert J.; Dumitrescu, Logan; Love, Shelly-Ann; Matise, Tara C.; Hindorff, Lucia A.; Fowke, Jay H.; Schumacher, Fredrick R.; Beebe-Dimmer, Jennifer; Chen, Chu; Hou, Lifang; Thomas, Fridtjof; Deelman, Ewa; Han, Ying; Peters, Ulrike; North, Kari E.; Heiss, Gerardo; Crawford, Dana C.; Haiman, Christopher A.; Wilkens, Lynne R.; Bush, William S.; Kooperberg, Charles; Cheng, Iona; Le Marchand, Loïc

    2014-01-01

    Background Multiple primary cancers account for ~16% of all incident cancers in the U.S.. While genome-wide association studies (GWAS) have identified many common genetic variants associated with various cancer sites, no study has examined the association of these genetic variants with risk of multiple primary cancers (MPC). Methods As part of the NHGRI Population Architecture using Genomics and Epidemiology (PAGE) study, we used data from the Multiethnic Cohort and Women’s Health Initiative. Incident MPC (IMPC) cases (n=1,385) were defined as participants diagnosed with >1 incident cancers after cohort entry. Participants diagnosed with only one incident cancer after cohort entry with follow-up equal to or longer than IMPC cases served as controls (single-index cancer controls; n= 9,626). Fixed-effects meta-analyses of unconditional logistic regression analyses were used to evaluate the association between cancer risk variants and IMPC risk. To account for multiple comparisons, we used the false positive report probability (FPRP) to determine statistical significance. Results A nicotine dependence-associated and lung cancer variant, CHRNA3 rs578776 (OR=1.16, 95% CI=1.05–1.26; p=0.004) and two breast cancer variants, EMBP1 rs11249433 and TOX3 rs3803662 (OR=1.16, 95% CI=1.04–1.28; p=0.005 and OR=1.13, 95% CI=1.03–1.23; p=0.006) were significantly associated with risk of IMPC. The associations for rs578776 and rs11249433 remained (p<0.05) after removing subjects who had lung or breast cancers, respectively (p-values≤0.046). These associations did not show significant heterogeneity by smoking status (p-heterogeneity≥0.53). Conclusions Our study has identified rs578776 and rs11249433 as risk variants for IMPC. Impact These findings may help to identify genetic regions associated with IMPC risk. PMID:25139936

  20. Genetic determinants of lipid traits in diverse populations from the population architecture using genomics and epidemiology (PAGE) study.

    PubMed

    Dumitrescu, Logan; Carty, Cara L; Taylor, Kira; Schumacher, Fredrick R; Hindorff, Lucia A; Ambite, José L; Anderson, Garnet; Best, Lyle G; Brown-Gentry, Kristin; Bůžková, Petra; Carlson, Christopher S; Cochran, Barbara; Cole, Shelley A; Devereux, Richard B; Duggan, Dave; Eaton, Charles B; Fornage, Myriam; Franceschini, Nora; Haessler, Jeff; Howard, Barbara V; Johnson, Karen C; Laston, Sandra; Kolonel, Laurence N; Lee, Elisa T; MacCluer, Jean W; Manolio, Teri A; Pendergrass, Sarah A; Quibrera, Miguel; Shohet, Ralph V; Wilkens, Lynne R; Haiman, Christopher A; Le Marchand, Loïc; Buyske, Steven; Kooperberg, Charles; North, Kari E; Crawford, Dana C

    2011-06-01

    For the past five years, genome-wide association studies (GWAS) have identified hundreds of common variants associated with human diseases and traits, including high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), and triglyceride (TG) levels. Approximately 95 loci associated with lipid levels have been identified primarily among populations of European ancestry. The Population Architecture using Genomics and Epidemiology (PAGE) study was established in 2008 to characterize GWAS-identified variants in diverse population-based studies. We genotyped 49 GWAS-identified SNPs associated with one or more lipid traits in at least two PAGE studies and across six racial/ethnic groups. We performed a meta-analysis testing for SNP associations with fasting HDL-C, LDL-C, and ln(TG) levels in self-identified European American (~20,000), African American (~9,000), American Indian (~6,000), Mexican American/Hispanic (~2,500), Japanese/East Asian (~690), and Pacific Islander/Native Hawaiian (~175) adults, regardless of lipid-lowering medication use. We replicated 55 of 60 (92%) SNP associations tested in European Americans at p<0.05. Despite sufficient power, we were unable to replicate ABCA1 rs4149268 and rs1883025, CETP rs1864163, and TTC39B rs471364 previously associated with HDL-C and MAFB rs6102059 previously associated with LDL-C. Based on significance (p<0.05) and consistent direction of effect, a majority of replicated genotype-phentoype associations for HDL-C, LDL-C, and ln(TG) in European Americans generalized to African Americans (48%, 61%, and 57%), American Indians (45%, 64%, and 77%), and Mexican Americans/Hispanics (57%, 56%, and 86%). Overall, 16 associations generalized across all three populations. For the associations that did not generalize, differences in effect sizes, allele frequencies, and linkage disequilibrium offer clues to the next generation of association studies for these traits.

  1. Genome-wide SNP and microsatellite variation illuminate population-level epidemiology in the Leishmania donovani species complex

    PubMed Central

    Downing, Tim; Stark, Olivia; Vanaerschot, Manu; Imamura, Hideo; Sanders, Mandy; Decuypere, Saskia; de Doncker, Simonne; Maes, Ilse; Rijal, Suman; Sundar, Shyam; Dujardin, Jean-Claude; Berriman, Matthew; Schönian, Gabriele

    2012-01-01

    The species of the Leishmania donovani species complex cause visceral leishmaniasis, a debilitating infectious disease transmitted by sandflies. Understanding molecular changes associated with population structure in these parasites can help unravel their epidemiology and spread in humans. In this study, we used a panel of standard microsatellite loci and genome-wide SNPs to investigate population-level diversity in L. donovani strains recently isolated from a small geographic area spanning India, Bihar and Nepal, and compared their variation to that found in diverse strains of the L. donovani complex isolates from Europe, Africa and Asia. Microsatellites and SNPs could clearly resolve the phylogenetic relationships of the strains between continents, and microsatellite phylogenies indicated that certain older Indian strains were closely related to African strains. In the context of the anti-malaria spraying campaigns in the 1960s, this was consistent with a pattern of episodic population size contractions and clonal expansions in these parasites that was supported by population history simulations. In sharp contrast to the low resolution provided by microsatellites, SNPs retained a much more fine-scale resolution of population-level variability to the extent that they identified four different lineages from the same region one of which was more closely related to African and European strains than to Indian or Nepalese ones. Joining results of in vitro testing the antimonial drug sensitivity with the phylogenetic signals from the SNP data highlighted protein-level mutations revealing a distinct drug-resistant group of Nepalese and Indian L. donovani. This study demonstrates the power of genomic data for exploring parasite population structure. Furthermore, markers defining different genetic groups have been discovered that could potentially be applied to investigate drug resistance in clinical Leishmania strains. PMID:22119748

  2. 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

  3. Genomic epidemiology reveals multiple introductions of Zika virus into the United States.

    PubMed

    Grubaugh, Nathan D; Ladner, Jason T; Kraemer, Moritz U G; Dudas, Gytis; Tan, Amanda L; Gangavarapu, Karthik; Wiley, Michael R; White, Stephen; Thézé, Julien; Magnani, Diogo M; Prieto, Karla; Reyes, Daniel; Bingham, Andrea M; Paul, Lauren M; Robles-Sikisaka, Refugio; Oliveira, Glenn; Pronty, Darryl; Barcellona, Carolyn M; Metsky, Hayden C; Baniecki, Mary Lynn; Barnes, Kayla G; Chak, Bridget; Freije, Catherine A; Gladden-Young, Adrianne; Gnirke, Andreas; Luo, Cynthia; MacInnis, Bronwyn; Matranga, Christian B; Park, Daniel J; Qu, James; Schaffner, Stephen F; Tomkins-Tinch, Christopher; West, Kendra L; Winnicki, Sarah M; Wohl, Shirlee; Yozwiak, Nathan L; Quick, Joshua; Fauver, Joseph R; Khan, Kamran; Brent, Shannon E; Reiner, Robert C; Lichtenberger, Paola N; Ricciardi, Michael J; Bailey, Varian K; Watkins, David I; Cone, Marshall R; Kopp, Edgar W; Hogan, Kelly N; Cannons, Andrew C; Jean, Reynald; Monaghan, Andrew J; Garry, Robert F; Loman, Nicholas J; Faria, Nuno R; Porcelli, Mario C; Vasquez, Chalmers; Nagle, Elyse R; Cummings, Derek A T; Stanek, Danielle; Rambaut, Andrew; Sanchez-Lockhart, Mariano; Sabeti, Pardis C; Gillis, Leah D; Michael, Scott F; Bedford, Trevor; Pybus, Oliver G; Isern, Sharon; Palacios, Gustavo; Andersen, Kristian G

    2017-06-15

    Zika virus (ZIKV) is causing an unprecedented epidemic linked to severe congenital abnormalities. In July 2016, mosquito-borne ZIKV transmission was reported in the continental United States; since then, hundreds of locally acquired infections have been reported in Florida. To gain insights into the timing, source, and likely route(s) of ZIKV introduction, we tracked the virus from its first detection in Florida by sequencing ZIKV genomes from infected patients and Aedes aegypti mosquitoes. We show that at least 4 introductions, but potentially as many as 40, contributed to the outbreak in Florida and that local transmission is likely to have started in the spring of 2016-several months before its initial detection. By analysing surveillance and genetic data, we show that ZIKV moved among transmission zones in Miami. Our analyses show that most introductions were linked to the Caribbean, a finding corroborated by the high incidence rates and traffic volumes from the region into the Miami area. Our study provides an understanding of how ZIKV initiates transmission in new regions.

  4. Genomic epidemiology reveals multiple introductions of Zika virus into the United States

    NASA Astrophysics Data System (ADS)

    Grubaugh, Nathan D.; Ladner, Jason T.; Kraemer, Moritz U. G.; Dudas, Gytis; Tan, Amanda L.; Gangavarapu, Karthik; Wiley, Michael R.; White, Stephen; Thézé, Julien; Magnani, Diogo M.; Prieto, Karla; Reyes, Daniel; Bingham, Andrea M.; Paul, Lauren M.; Robles-Sikisaka, Refugio; Oliveira, Glenn; Pronty, Darryl; Barcellona, Carolyn M.; Metsky, Hayden C.; Baniecki, Mary Lynn; Barnes, Kayla G.; Chak, Bridget; Freije, Catherine A.; Gladden-Young, Adrianne; Gnirke, Andreas; Luo, Cynthia; Macinnis, Bronwyn; Matranga, Christian B.; Park, Daniel J.; Qu, James; Schaffner, Stephen F.; Tomkins-Tinch, Christopher; West, Kendra L.; Winnicki, Sarah M.; Wohl, Shirlee; Yozwiak, Nathan L.; Quick, Joshua; Fauver, Joseph R.; Khan, Kamran; Brent, Shannon E.; Reiner, Robert C.; Lichtenberger, Paola N.; Ricciardi, Michael J.; Bailey, Varian K.; Watkins, David I.; Cone, Marshall R.; Kopp, Edgar W.; Hogan, Kelly N.; Cannons, Andrew C.; Jean, Reynald; Monaghan, Andrew J.; Garry, Robert F.; Loman, Nicholas J.; Faria, Nuno R.; Porcelli, Mario C.; Vasquez, Chalmers; Nagle, Elyse R.; Cummings, Derek A. T.; Stanek, Danielle; Rambaut, Andrew; Sanchez-Lockhart, Mariano; Sabeti, Pardis C.; Gillis, Leah D.; Michael, Scott F.; Bedford, Trevor; Pybus, Oliver G.; Isern, Sharon; Palacios, Gustavo; Andersen, Kristian G.

    2017-06-01

    Zika virus (ZIKV) is causing an unprecedented epidemic linked to severe congenital abnormalities. In July 2016, mosquito-borne ZIKV transmission was reported in the continental United States; since then, hundreds of locally acquired infections have been reported in Florida. To gain insights into the timing, source, and likely route(s) of ZIKV introduction, we tracked the virus from its first detection in Florida by sequencing ZIKV genomes from infected patients and Aedes aegypti mosquitoes. We show that at least 4 introductions, but potentially as many as 40, contributed to the outbreak in Florida and that local transmission is likely to have started in the spring of 2016—several months before its initial detection. By analysing surveillance and genetic data, we show that ZIKV moved among transmission zones in Miami. Our analyses show that most introductions were linked to the Caribbean, a finding corroborated by the high incidence rates and traffic volumes from the region into the Miami area. Our study provides an understanding of how ZIKV initiates transmission in new regions.

  5. Unusual Legionnaires' outbreak in cool, dry Western Canada: an investigation using genomic epidemiology.

    PubMed

    Knox, N C; Weedmark, K A; Conly, J; Ensminger, A W; Hosein, F S; Drews, S J

    2017-01-01

    An outbreak of Legionnaires' disease occurred in an inner city district in Calgary, Canada. This outbreak spanned a 3-week period in November-December 2012, and a total of eight cases were identified. Four of these cases were critically ill requiring intensive care admission but there was no associated mortality. All cases tested positive for Legionella pneumophila serogroup 1 (LP1) by urinary antigen testing. Five of the eight patients were culture positive for LP1 from respiratory specimens. These isolates were further identified as Knoxville monoclonal subtype and sequence subtype ST222. Whole-genome sequencing revealed that the isolates differed by no more than a single vertically acquired single nucleotide variant, supporting a single point-source outbreak. Hypothesis-based environmental investigation and sampling was conducted; however, a definitive source was not identified. Geomapping of case movements within the affected urban sector revealed a 1·0 km common area of potential exposure, which coincided with multiple active construction sites that used water spray to minimize transient dust. This community point-source Legionnaires' disease outbreak is unique due to its ST222 subtype and occurrence in a relatively dry and cold weather setting in Western Canada. This report suggests community outbreaks of Legionella should not be overlooked as a possibility during late autumn and winter months in the Northern Hemisphere.

  6. 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

  7. [An evaluation of sampling design for estimating an epidemiologic volume of diabetes and for assessing present status of its control in Korea].

    PubMed

    Lee, Ji-Sung; Kim, Jaiyong; Baik, Sei-Hyun; Park, Ie-Byung; Lee, Juneyoung

    2009-03-01

    An appropriate sampling strategy for estimating an epidemiologic volume of diabetes has been evaluated through a simulation. We analyzed about 250 million medical insurance claims data submitted to the Health Insurance Review & Assessment Service with diabetes as principal or subsequent diagnoses, more than or equal to once per year, in 2003. The database was re-constructed to a 'patient-hospital profile' that had 3,676,164 cases, and then to a 'patient profile' that consisted of 2,412,082 observations. The patient profile data was then used to test the validity of a proposed sampling frame and methods of sampling to develop diabetic-related epidemiologic indices. Simulation study showed that a use of a stratified two-stage cluster sampling design with a total sample size of 4,000 will provide an estimate of 57.04% (95% prediction range, 49.83 - 64.24%) for a treatment prescription rate of diabetes. The proposed sampling design consists, at first, stratifying the area of the nation into "metropolitan/city/county" and the types of hospital into "tertiary/secondary/primary/clinic" with a proportion of 5:10:10:75. Hospitals were then randomly selected within the strata as a primary sampling unit, followed by a random selection of patients within the hospitals as a secondly sampling unit. The difference between the estimate and the parameter value was projected to be less than 0.3%. The sampling scheme proposed will be applied to a subsequent nationwide field survey not only for estimating the epidemiologic volume of diabetes but also for assessing the present status of nationwide diabetes control.

  8. Serious fungal infections in Korea.

    PubMed

    Huh, K; Ha, Y E; Denning, D W; Peck, K R

    2017-02-04

    Information on the incidence and prevalence of fungal infections is of critical value in public health policy. However, nationwide epidemiological data on fungal infections are scarce, due to a lack of surveillance and funding. The objective of this study was to estimate the disease burden of fungal infections in the Republic of Korea. An actuarial approach using a deterministic model was used for the estimation. Data on the number of populations at risk and the frequencies of fungal infections in those populations were obtained from national statistics reports and epidemiology papers. Approximately 1 million people were estimated to be affected by fungal infections every year. The burdens of candidemia (4.12 per 100,000), cryptococcal meningitis (0.09 per 100,000), and Pneumocystis pneumonia (0.51 per 100,000) in South Korea were estimated to be comparable to those in other countries. The prevalence of chronic pulmonary aspergillosis (22.4 per 100,000) was markedly high, probably due to the high burden of tuberculosis in Korea. The low burdens of allergic bronchopulmonary aspergillosis (56.9 per 100,000) and severe asthma with fungal sensitization (75.1 per 100,000) warrant further study. Oral candidiasis (539 per 100,000) was estimated to affect a much larger population than noted in previous studies. Our work provides valuable insight on the epidemiology of fungal infections; however, additional studies are needed.

  9. 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).

  10. 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. © 2015 Institute of Food Technologists®

  11. Epidemiology and full genome sequence analysis of H1N1pdm09 from Northeast China.

    PubMed

    Li, Xiaoyan; Kong, Mei; Chen, Jinying; Su, Xu; Zou, Ming; Guo, Liru; Li, Lin; Ding, Jianqing

    2013-10-01

    Pandemic influenza A (H1N1) 2009 virus (H1N1pdm09) was a novel tri-assortment virus that emerged in Mexico and North America in 2009 and caused the first influenza pandemic in the 21st century. This study investigated the prevalence pattern and molecular characteristics of H1N1pdm09 in three continuous years from April 2009 to March 2012 in populations of Tianjin, Northeast China. Totally, 3,068 influenza viruses (25.4 %) were detected from 12,089 respiratory specimens. Among them, 41.4 % (1,269/3,068) were H1N1pdm09 positive. 15.1 % (192/1,269) severe respiratory infection cases were H1N1pdm09 positive. H1N1pdm09 was the predominant prevalence subtype in October 2009-March 2010 (69.1 %, 930/1,346) and October 2010-March 2011 (42.1 %, 220/523). Eight isolated H1N1pdm09 viruses from severe infection/death cases in three different years were selected to sequence the whole genome through splicing the sequences following 46 PCRs. HA sequences of seven H1N1pdm09 isolates from mild infection cases were detected. Phylogenetic analysis showed that HA, NA, M, NP and NS genes of H1N1pdm09 viruses gathered together with swine influenza A (H1N1), whereas PB2 and PA genes originated from avian influenza virus, and PB1 gene originated from human seasonal influenza virus. Identity analysis indicated that all the genes were highly conserved. Compared with vaccine strain A/California/07/2009(H1N1), the maximal mutation gene was HA (0.7-2.6 %), then NA (0.6-1.7 %), last one was M (mutation rate 0-0.6 %). More site substitutions were observed in 2011 isolates than in 2009 and 2010 isolates of HA (p = 0.002), NA (p = 0.003) and PA (p = 0.001) proteins. The amino acid substitution rates were varied among eight gene segments, ranging from 7.39 × 10(-4) for PB2 to 7.40 × 10(-3) for NA. The higher d N / d S rates were observed in HA, PA and NS segments in H1N1pdm09 in Tianjin. Three HA amino acid site substitutions occurred at the HA receptor-binding sites and

  12. 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

  13. Genetic Determinants of Lipid Traits in Diverse Populations from the Population Architecture using Genomics and Epidemiology (PAGE) Study

    PubMed Central

    Dumitrescu, Logan; Carty, Cara L.; Taylor, Kira; Schumacher, Fredrick R.; Hindorff, Lucia A.; Ambite, José L.; Anderson, Garnet; Best, Lyle G.; Brown-Gentry, Kristin; Bůžková, Petra; Carlson, Christopher S.; Cochran, Barbara; Cole, Shelley A.; Devereux, Richard B.; Duggan, Dave; Eaton, Charles B.; Fornage, Myriam; Franceschini, Nora; Haessler, Jeff; Howard, Barbara V.; Johnson, Karen C.; Laston, Sandra; Kolonel, Laurence N.; Lee, Elisa T.; MacCluer, Jean W.; Manolio, Teri A.; Pendergrass, Sarah A.; Quibrera, Miguel; Shohet, Ralph V.; Wilkens, Lynne R.; Haiman, Christopher A.; Le Marchand, Loïc; Buyske, Steven; Kooperberg, Charles; North, Kari E.; Crawford, Dana C.

    2011-01-01

    For the past five years, genome-wide association studies (GWAS) have identified hundreds of common variants associated with human diseases and traits, including high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), and triglyceride (TG) levels. Approximately 95 loci associated with lipid levels have been identified primarily among populations of European ancestry. The Population Architecture using Genomics and Epidemiology (PAGE) study was established in 2008 to characterize GWAS–identified variants in diverse population-based studies. We genotyped 49 GWAS–identified SNPs associated with one or more lipid traits in at least two PAGE studies and across six racial/ethnic groups. We performed a meta-analysis testing for SNP associations with fasting HDL-C, LDL-C, and ln(TG) levels in self-identified European American (∼20,000), African American (∼9,000), American Indian (∼6,000), Mexican American/Hispanic (∼2,500), Japanese/East Asian (∼690), and Pacific Islander/Native Hawaiian (∼175) adults, regardless of lipid-lowering medication use. We replicated 55 of 60 (92%) SNP associations tested in European Americans at p<0.05. Despite sufficient power, we were unable to replicate ABCA1 rs4149268 and rs1883025, CETP rs1864163, and TTC39B rs471364 previously associated with HDL-C and MAFB rs6102059 previously associated with LDL-C. Based on significance (p<0.05) and consistent direction of effect, a majority of replicated genotype-phentoype associations for HDL-C, LDL-C, and ln(TG) in European Americans generalized to African Americans (48%, 61%, and 57%), American Indians (45%, 64%, and 77%), and Mexican Americans/Hispanics (57%, 56%, and 86%). Overall, 16 associations generalized across all three populations. For the associations that did not generalize, differences in effect sizes, allele frequencies, and linkage disequilibrium offer clues to the next generation of association studies for these traits. PMID:21738485

  14. Genetic Variation and Reproductive Timing: African American Women from the Population Architecture Using Genomics and Epidemiology (PAGE) Study

    PubMed Central

    Carty, Cara L.; Franceschini, Nora; Fernández-Rhodes, Lindsay; Young, Alicia; Cheng, Iona; Ritchie, Marylyn D.; Haiman, Christopher A.; Wilkens, Lynne; ChunyuanWu; Matise, Tara C.; Carlson, Christopher S.; Brennan, Kathleen; Park, Amy; Rajkovic, Aleksandar; Hindorff, Lucia A.

    2013-01-01

    Age at menarche (AM) and age at natural menopause (ANM) define the boundaries of the reproductive lifespan in women. Their timing is associated with various diseases, including cancer and cardiovascular disease. Genome-wide association studies have identified several genetic variants associated with either AM or ANM in populations of largely European or Asian descent women. The extent to which these associations generalize to diverse populations remains unknown. Therefore, we sought to replicate previously reported AM and ANM findings and to identify novel AM and ANM variants using the Metabochip (n = 161,098 SNPs) in 4,159 and 1,860 African American women, respectively, in the Women’s Health Initiative (WHI) and Atherosclerosis Risk in Communities (ARIC) studies, as part of the Population Architecture using Genomics and Epidemiology (PAGE) Study. We replicated or generalized one previously identified variant for AM, rs1361108/CENPW, and two variants for ANM, rs897798/BRSK1 and rs769450/APOE, to our African American cohort. Overall, generalization of the majority of previously-identified variants for AM and ANM, including LIN28B and MCM8, was not observed in this African American sample. We identified three novel loci associated with ANM that reached significance after multiple testing correction (LDLR rs189596789, p = 5×10−08; KCNQ1 rs79972789, p = 1.9×10−07; COL4A3BP rs181686584, p = 2.9×10−07). Our most significant AM association was upstream of RSF1, a gene implicated in ovarian and breast cancers (rs11604207, p = 1.6×10−06). While most associations were identified in either AM or ANM, we did identify genes suggestively associated with both: PHACTR1 and ARHGAP42. The lack of generalization coupled with the potentially novel associations identified here emphasize the need for additional genetic discovery efforts for AM and ANM in diverse populations. PMID:23424626

  15. A Comparison of the Clinical and Epidemiological Characteristics of Adult Patients with Laboratory-Confirmed Influenza A or B during the 2011–2012 Influenza Season in Korea: A Multi-Center Study

    PubMed Central

    Wie, Seong-Heon; So, Byung Hak; Song, Joon Young; Cheong, Hee Jin; Seo, Yu Bin; Choi, Sung Hyuk; Noh, Ji Yun; Baek, Ji Hyeon; Lee, Jin Soo; Kim, Hyo Youl; Kim, Young Keun; Choi, Won Suk; Lee, Jacob; Jeong, Hye Won; Kim, Woo Joo

    2013-01-01

    Background During the 2011/2012 winter influenza season in the Republic of Korea, influenza A (H3N2) was the predominant virus in the first peak period of influenza activity during the second half of January 2012. On the other hand, influenza B was the predominant virus in the second peak period of influenza activity during the second half of March 2012. The objectives of this study were to compare the clinical and epidemiological characteristics of patients with laboratory-confirmed influenza A or influenza B. Methodology/Principal Findings We analyzed data from 2,129 adult patients with influenza-like illnesses who visited the emergency rooms of seven university hospitals in Korea from October 2011 to May 2012. Of 850 patients with laboratory-confirmed influenza, 656 (77.2%) had influenza A (H3N2), and 194 (22.8%) influenza B. Age, and the frequencies of cardiovascular disorders, diabetes, hypertension were significantly higher in patients with influenza A (H3N2) (P<0.05). The frequencies of leukopenia or thrombocytopenia in patients with influenza B at initial presentation were statistically higher than those in patients with influenza A (H3N2) (P<0.05). The rate of hospitalization, and length of hospital stay were statistically higher in patients with influenza A (H3N2) (P<0.05), and of the 79 hospitalized patients, the frequency of diabetes, hypertension, cases having at least one of the comorbid conditions, and the proportion of elderly were significantly higher in patients with influenza A (H3N2) (P<0.05). Conclusions The proportion of males to females and elderly population were significantly higher for influenza A (H3N2) patients group compared with influenza B group. Hypertension, diabetes, chronic lung diseases, cardiovascular disorders, and neuromuscular diseases were independently associated with hospitalization due to influenza. Physicians should assess and treat the underlying comorbid conditions as well as influenza viral infections for the

  16. Neck Circumference and Incidence of Diabetes Mellitus over 10 Years in the Korean Genome and Epidemiology Study (KoGES).

    PubMed

    Cho, Nam H; Oh, Tae Jung; Kim, Kyoung Min; Choi, Sung Hee; Lee, Jae Ho; Park, Kyong Soo; Jang, Hak Chul; Kim, Jong Yeol; Lee, Hong Kyu; Lim, Soo

    2015-12-18

    Neck circumference, a proxy for upper-body fat, may be a unique fat depot that indicates metabolic risk beyond whole body fat. We investigated whether neck circumference is associated with development of diabetes mellitus (DM) in a subset of data with Korean Genome and Epidemiology Study (n = 3521, age range = 42-71 years). Nondiabetic subjects at the baseline were categorized into 4 groups (Q1-Q4) according to their neck circumference. Parameters related with β-cell function and insulin resistance including Epworth sleepiness scale and snoring habit were examined. The development of DM was confirmed biannually based on a 75-g oral glucose tolerance test. Over the 10 years, 2623 (74.5%) among 3521 subjects were followed-up. Among them, 632 (24.1%) developed DM. The incidence of DM increased from 17.6% in Q1 to 18.2% in Q2, to 25.4% in Q3, and to 36.0% in Q4 (P < 0.001). After adjusting for most risk factors related with DM, the relative risks of DM development were 0.989 (95% confidence interval, 0.638-1.578), 1.660 (1.025-2.687), and 1.746 (1.037-2.942) in men and 0.939 (0.540-1.769), 1.518 (0.808-2.853), and 2.077 (1.068-4.038) in women in Q2, Q3, and Q4, respectively when compared to Q1. This finding indicates negative impact from large neck circumference in the development of DM.

  17. Sleep duration and chronic kidney disease: The Korean Genome and Epidemiology Study (KoGES)-Kangwha study

    PubMed Central

    Choi, Hansol; Kim, Hyeon Chang; Lee, Joo Young; Lee, Ju-Mi; Choi, Dong Phil; Suh, Il

    2017-01-01

    Background/Aims Sleep duration affects health in various ways. The objective of this study was to investigate the associations of sleep duration with chronic kidney disease (CKD) in a Korean adult population. Methods This cross-sectional analysis was conducted for total of 1,360 participants who completed baseline health examinations for the Korean Genome and Epidemiology Study-Kangwha study in 2010 to 2011. Sleep habits were measured by an interviewer-assisted questionnaire. Sleep duration was calculated based on the number of hours per day participants had slept over the past 1 year. CKD was defined as either proteinuria or estimated glomerular filtration rate (eGFR) < 60 mL/min/1.73 m2. Multiple logistic regression models were applied to examine associations between sleep duration and CKD. Results Women with very long sleep duration (≥ 9 hours/day) were at significantly increased odds for having high serum creatinine (odds ratio [OR], 2.936; 95% confidence interval [CI], 1.176 to 7.326), low eGFR (OR, 3.320; 95% CI, 1.372 to 8.034), and CKD (OR, 3.112; 95% CI, 1.315 to 7.363), compared those with a typical sleep duration (7 to < 8 hours/day), after adjusting for sociodemographic status, socioeconomic status, health behaviors, comorbidities, and sleep quality. Among women, for every 1 hour increase in sleep duration per day, there was a 24.6% increase in the presence of CKD (OR, 1.246; 95% CI, 1.019 to 1.523). However, among men, sleep duration was not significantly associated with CKD. Conclusions Very long sleep duration was independently associated with a higher prevalence of CKD among Korean women. Gender may influence this association. PMID:28192891

  18. Genomic Epidemiology of NDM-1-Encoding Plasmids in Latin American Clinical Isolates Reveals Insights into the Evolution of Multidrug Resistance.

    PubMed

    Marquez-Ortiz, Ricaurte Alejandro; Haggerty, Leanne; Olarte, Narda; Duarte, Carolina; Garza-Ramos, Ulises; Silva-Sanchez, Jesus; Castro, Betsy E; Sim, Eby M; Beltran, Mauricio; Moncada, María V; Valderrama, Alberto; Castellanos, Jaime E; Charles, Ian G; Vanegas, Natasha; Escobar-Perez, Javier; Petty, Nicola K

    2017-06-01

    Bacteria that produce the broad-spectrum Carbapenem antibiotic New Delhi Metallo-β-lactamase (NDM) place a burden on health care systems worldwide, due to the limited treatment options for infections caused by them and the rapid global spread of this antibiotic resistance mechanism. Although it is believed that the associated resistance gene blaNDM-1 originated in Acinetobacter spp., the role of Enterobacteriaceae in its dissemination remains unclear. In this study, we used whole genome sequencing to investigate the dissemination dynamics of blaNDM-1-positive plasmids in a set of 21 clinical NDM-1-positive isolates from Colombia and Mexico (Providencia rettgeri, Klebsiella pneumoniae, and Acinetobacter baumannii) as well as six representative NDM-1-positive Escherichia coli transconjugants. Additionally, the plasmids from three representative P. rettgeri isolates were sequenced by PacBio sequencing and finished. Our results demonstrate the presence of previously reported plasmids from K. pneumoniae and A. baumannii in different genetic backgrounds and geographically distant locations in Colombia. Three new previously unclassified plasmids were also identified in P. rettgeri from Colombia and Mexico, plus an interesting genetic link between NDM-1-positive P. rettgeri from distant geographic locations (Canada, Mexico, Colombia, and Israel) without any reported epidemiological links was discovered. Finally, we detected a relationship between plasmids present in P. rettgeri and plasmids from A. baumannii and K. pneumoniae. Overall, our findings suggest a Russian doll model for the dissemination of blaNDM-1 in Latin America, with P. rettgeri playing a central role in this process, and reveal new insights into the evolution and dissemination of plasmids carrying such antibiotic resistance genes. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  19. Genomic Epidemiology of NDM-1-Encoding Plasmids in Latin American Clinical Isolates Reveals Insights into the Evolution of Multidrug Resistance

    PubMed Central

    Marquez-Ortiz, Ricaurte Alejandro; Haggerty, Leanne; Olarte, Narda; Duarte, Carolina; Garza-Ramos, Ulises; Silva-Sanchez, Jesus; Castro, Betsy E.; Sim, Eby M.; Beltran, Mauricio; Moncada, María V.; Valderrama, Alberto; Castellanos, Jaime E.; Charles, Ian G.; Vanegas, Natasha

    2017-01-01

    Abstract Bacteria that produce the broad-spectrum Carbapenem antibiotic New Delhi Metallo-β-lactamase (NDM) place a burden on health care systems worldwide, due to the limited treatment options for infections caused by them and the rapid global spread of this antibiotic resistance mechanism. Although it is believed that the associated resistance gene blaNDM-1 originated in Acinetobacter spp., the role of Enterobacteriaceae in its dissemination remains unclear. In this study, we used whole genome sequencing to investigate the dissemination dynamics of blaNDM-1-positive plasmids in a set of 21 clinical NDM-1-positive isolates from Colombia and Mexico (Providencia rettgeri, Klebsiella pneumoniae, and Acinetobacter baumannii) as well as six representative NDM-1-positive Escherichia coli transconjugants. Additionally, the plasmids from three representative P. rettgeri isolates were sequenced by PacBio sequencing and finished. Our results demonstrate the presence of previously reported plasmids from K. pneumoniae and A. baumannii in different genetic backgrounds and geographically distant locations in Colombia. Three new previously unclassified plasmids were also identified in P. rettgeri from Colombia and Mexico, plus an interesting genetic link between NDM-1-positive P. rettgeri from distant geographic locations (Canada, Mexico, Colombia, and Israel) without any reported epidemiological links was discovered. Finally, we detected a relationship between plasmids present in P. rettgeri and plasmids from A. baumannii and K. pneumoniae. Overall, our findings suggest a Russian doll model for the dissemination of blaNDM-1 in Latin America, with P. rettgeri playing a central role in this process, and reveal new insights into the evolution and dissemination of plasmids carrying such antibiotic resistance genes. PMID:28854628

  20. Sleep duration and chronic kidney disease: The Korean Genome and Epidemiology Study (KoGES)-Kangwha study.

    PubMed

    Choi, Hansol; Kim, Hyeon Chang; Lee, Joo Young; Lee, Ju-Mi; Choi, Dong Phil; Suh, Il

    2017-03-01

    Sleep duration affects health in various ways. The objective of this study was to investigate the associations of sleep duration with chronic kidney disease (CKD) in a Korean adult population. This cross-sectional analysis was conducted for total of 1,360 participants who completed baseline health examinations for the Korean Genome and Epidemiology Study-Kangwha study in 2010 to 2011. Sleep habits were measured by an interviewer-assisted questionnaire. Sleep duration was calculated based on the number of hours per day participants had slept over the past 1 year. CKD was defined as either proteinuria or estimated glomerular filtration rate (eGFR) < 60 mL/min/1.73 m(2). Multiple logistic regression models were applied to examine associations between sleep duration and CKD. Women with very long sleep duration (≥ 9 hours/day) were at significantly increased odds for having high serum creatinine (odds ratio [OR], 2.936; 95% confidence interval [CI], 1.176 to 7.326), low eGFR (OR, 3.320; 95% CI, 1.372 to 8.034), and CKD (OR, 3.112; 95% CI, 1.315 to 7.363), compared those with a typical sleep duration (7 to < 8 hours/day), after adjusting for sociodemographic status, socioeconomic status, health behaviors, comorbidities, and sleep quality. Among women, for every 1 hour increase in sleep duration per day, there was a 24.6% increase in the presence of CKD (OR, 1.246; 95% CI, 1.019 to 1.523). However, among men, sleep duration was not significantly associated with CKD. Very long sleep duration was independently associated with a higher prevalence of CKD among Korean women. Gender may influence this association.

  1. Genome Dynamics and Molecular Infection Epidemiology of Multidrug-Resistant Helicobacter pullorum Isolates Obtained from Broiler and Free-Range Chickens in India

    PubMed Central

    Qumar, Shamsul; Majid, Mohammad; Kumar, Narender; Tiwari, Sumeet K.; Semmler, Torsten; Devi, Savita; Baddam, Ramani; Hussain, Arif; Shaik, Sabiha

    2016-01-01

    ABSTRACT Some life-threatening, foodborne, and zoonotic infections are transmitted through poultry birds. Inappropriate and indiscriminate use of antimicrobials in the livestock industry has led to an increased prevalence of multidrug-resistant bacteria with epidemic potential. Here, we present a functional molecular epidemiological analysis entailing the phenotypic and whole-genome sequence-based characterization of 11 H. pullorum isolates from broiler and free-range chickens sampled from retail wet markets in Hyderabad City, India. Antimicrobial susceptibility tests revealed all of the isolates to be resistant to multiple antibiotic classes such as fluoroquinolones, cephalosporins, sulfonamides, and macrolides. The isolates were also found to be extended-spectrum β-lactamase producers and were even resistant to clavulanic acid. Whole-genome sequencing and comparative genomic analysis of these isolates revealed the presence of five or six well-characterized antimicrobial resistance genes, including those encoding a resistance-nodulation-division efflux pump(s). Phylogenetic analysis combined with pan-genome analysis revealed a remarkable degree of genetic diversity among the isolates from free-range chickens; in contrast, a high degree of genetic similarity was observed among broiler chicken isolates. Comparative genomic analysis of all publicly available H. pullorum genomes, including our isolates (n = 16), together with the genomes of 17 other Helicobacter species, revealed a high number (8,560) of H. pullorum-specific protein-encoding genes, with an average of 535 such genes per isolate. In silico virulence screening identified 182 important virulence genes and also revealed high strain-specific gene content in isolates from free-range chickens (average, 34) compared to broiler chicken isolates. A significant prevalence of prophages (ranging from 1 to 9) and a significant presence of genomic islands (0 to 4) were observed in free-range and broiler chicken

  2. 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.

  3. High-quality draft genome sequence of Flavobacterium suncheonense GH29-5T (DSM 17707T) isolated from greenhouse soil in South Korea, and emended description of Flavobacterium suncheonense GH29-5T

    DOE PAGES

    Tashkandy, Nisreen; Sabban, Sari; Fakieh, Mohammad; ...

    2016-06-16

    Flavobacterium suncheonense is a member of the family Flavobacteriaceae in the phylum Bacteroidetes. Strain GH29-5 T (DSM 17707 T ) was isolated from greenhouse soil in Suncheon, South Korea. F. suncheonense GH29-5 T is part of the Genomic Encyclopedia of Bacteria and Archaea project. The 2,880,663 bp long draft genome consists of 54 scaffolds with 2739 protein-coding genes and 82 RNA genes. The genome of strain GH29-5 T has 117 genes encoding peptidases but a small number of genes encoding carbohydrate active enzymes (51 CAZymes). Metallo and serine peptidases were found most frequently. Among CAZymes, eight glycoside hydrolase families, ninemore » glycosyl transferase families, two carbohydrate binding module families and four carbohydrate esterase families were identified. Suprisingly, polysaccharides utilization loci (PULs) were not found in strain GH29-5 T . Based on the coherent physiological and genomic characteristics we suggest that F. suncheonense GH29-5 T feeds rather on proteins than saccharides and lipids.« less

  4. Genomic Epidemiology of Klebsiella pneumoniae in Italy and Novel Insights into the Origin and Global Evolution of Its Resistance to Carbapenem Antibiotics

    PubMed Central

    Gaiarsa, Stefano; Comandatore, Francesco; Gaibani, Paolo; Corbella, Marta; Dalla Valle, Claudia; Epis, Sara; Scaltriti, Erika; Carretto, Edoardo; Farina, Claudio; Labonia, Maria; Landini, Maria Paola; Sambri, Vittorio; Bandi, Claudio; Marone, Piero

    2014-01-01

    Klebsiella pneumoniae is at the forefront of antimicrobial resistance for Gram-negative pathogenic bacteria, as strains resistant to third-generation cephalosporins and carbapenems are widely reported. The worldwide diffusion of these strains is of great concern due to the high morbidity and mortality often associated with K. pneumoniae infections in nosocomial environments. We sequenced the genomes of 89 K. pneumoniae strains isolated in six Italian hospitals. Strains were selected based on antibiotypes, regardless of multilocus sequence type, to obtain a picture of the epidemiology of K. pneumoniae in Italy. Thirty-one strains were carbapenem-resistant K. pneumoniae carbapenemase producers, 29 were resistant to third-generation cephalosporins, and 29 were susceptible to the aforementioned antibiotics. The genomes were compared to all of the sequences available in the databases, obtaining a data set of 319 genomes spanning the known diversity of K. pneumoniae worldwide. Bioinformatic analyses of this global data set allowed us to construct a whole-species phylogeny, to detect patterns of antibiotic resistance distribution, and to date the differentiation between specific clades of interest. Finally, we detected an ∼1.3-Mb recombination that characterizes all of the isolates of clonal complex 258, the most widespread carbapenem-resistant group of K. pneumoniae. The evolution of this complex was modeled, dating the newly detected and the previously reported recombination events. The present study contributes to the understanding of K. pneumoniae evolution, providing novel insights into its global genomic characteristics and drawing a dated epidemiological scenario for this pathogen in Italy. PMID:25367909

  5. Genomic DNA fingerprinting by pulsed-field gel electrophoresis as an epidemiological marker for study of nosocomial infections caused by methicillin-resistant Staphylococcus aureus.

    PubMed Central

    Ichiyama, S; Ohta, M; Shimokata, K; Kato, N; Takeuchi, J

    1991-01-01

    In this study, we have compared genomic DNA fingerprintings among isolates of methicillin-resistant Staphylococcus aureus (MRSA) by using pulsed-field gel electrophoresis (PFGE). Chromosomal fragments digested with SmaI were most suitable for the PFGE separation. SmaI cut genomic DNA into 15 to 20 fragments whose sizes ranged from about 30 to 1,500 kb. Thirty-one distinctive fragment patterns were identified in 111 infecting and colonizing MRSA isolates from six different hospitals in Japan. On the basis of the genomic typing by PFGE, we performed an epidemiological investigation of an outbreak of nosocomial MRSA infections among inpatients in Nagoya University Hospital. Ten types of chromosomal digestion were identified in the 20 strains isolated from 18 infected patients and 1 from colonized hospital personnel. According to the restriction patterns, we found that four types of these strains had caused epidemic infections among 13 patients in the outbreak. Two types (types 1 and 4) of the strains were involved in the death of five patients. The other infections were sporadic. The clarity and polymorphism of the chromosomal digestion patterns enabled us to discriminate between isolates which could not be differentiated by antibiogram or plasmid analysis. Classification of the genomic DNA fingerprinting patterns by PFGE is therefore proposed as a useful method for investigating the source, transmission, and spread of nosocomial MRSA infections. Images PMID:1757534

  6. Strategies to design and analyze targeted sequencing data: cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium Targeted Sequencing Study.

    PubMed

    Lin, Honghuang; Wang, Min; Brody, Jennifer A; Bis, Joshua C; Dupuis, Josée; Lumley, Thomas; McKnight, Barbara; Rice, Kenneth M; Sitlani, Colleen M; Reid, Jeffrey G; Bressler, Jan; Liu, Xiaoming; Davis, Brian C; Johnson, Andrew D; O'Donnell, Christopher J; Kovar, Christie L; Dinh, Huyen; Wu, Yuanqing; Newsham, Irene; Chen, Han; Broka, Andi; DeStefano, Anita L; Gupta, Mayetri; Lunetta, Kathryn L; Liu, Ching-Ti; White, Charles C; Xing, Chuanhua; Zhou, Yanhua; Benjamin, Emelia J; Schnabel, Renate B; Heckbert, Susan R; Psaty, Bruce M; Muzny, Donna M; Cupples, L Adrienne; Morrison, Alanna C; Boerwinkle, Eric

    2014-06-01

    Genome-wide association studies have identified thousands of genetic variants that influence a variety of diseases and health-related quantitative traits. However, the causal variants underlying the majority of genetic associations remain unknown. Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium Targeted Sequencing Study aims to follow up genome-wide association study signals and identify novel associations of the allelic spectrum of identified variants with cardiovascular-related traits. The study included 4231 participants from 3 CHARGE cohorts: the Atherosclerosis Risk in Communities Study, the Cardiovascular Health Study, and the Framingham Heart Study. We used a case-cohort design in which we selected both a random sample of participants and participants with extreme phenotypes for each of 14 traits. We sequenced and analyzed 77 genomic loci, which had previously been associated with ≥1 of 14 phenotypes. A total of 52 736 variants were characterized by sequencing and passed our stringent quality control criteria. For common variants (minor allele frequency ≥1%), we performed unweighted regression analyses to obtain P values for associations and weighted regression analyses to obtain effect estimates that accounted for the sampling design. For rare variants, we applied 2 approaches: collapsed aggregate statistics and joint analysis of variants using the sequence kernel association test. We sequenced 77 genomic loci in participants from 3 cohorts. We established a set of filters to identify high-quality variants and implemented statistical and bioinformatics strategies to analyze the sequence data and identify potentially functional variants within genome-wide association study loci. © 2014 American Heart Association, Inc.

  7. Complete mitochondrial genomes and nuclear ribosomal RNA operons of two species of Diplostomum (Platyhelminthes: Trematoda): a molecular resource for taxonomy and molecular epidemiology of important fish pathogens.

    PubMed

    Brabec, Jan; Kostadinova, Aneta; Scholz, Tomáš; Littlewood, D Timothy J

    2015-06-19

    The genus Diplostomum (Platyhelminthes: Trematoda: Diplostomidae) is a diverse group of freshwater parasites with complex life-cycles and global distribution. The larval stages are important pathogens causing eye fluke disease implicated in substantial impacts on natural fish populations and losses in aquaculture. However, the problematic species delimitation and difficulties in the identification of larval stages hamper the assessment of the distributional and host ranges of Diplostomum spp. and their transmission ecology. Total genomic DNA was isolated from adult worms and shotgun sequenced using Illumina MiSeq technology. Mitochondrial (mt) genomes and nuclear ribosomal RNA (rRNA) operons were assembled using established bioinformatic tools and fully annotated. Mt protein-coding genes and nuclear rRNA genes were subjected to phylogenetic analysis by maximum likelihood and the resulting topologies compared. We characterised novel complete mt genomes and nuclear rRNA operons of two closely related species, Diplostomum spathaceum and D. pseudospathaceum. Comparative mt genome assessment revealed that the cox1 gene and its 'barcode' region used for molecular identification are the most conserved regions; instead, nad4 and nad5 genes were identified as most promising molecular diagnostic markers. Using the novel data, we provide the first genome wide estimation of the phylogenetic relationships of the order Diplostomida, one of the two fundamental lineages of the Digenea. Analyses of the mitogenomic data invariably recovered the Diplostomidae as a sister lineage of the order Plagiorchiida rather than as a basal lineage of the Diplostomida as inferred in rDNA phylogenies; this was concordant with the mt gene order of Diplostomum spp. exhibiting closer match to the conserved gene order of the Plagiorchiida. Complete sequences of the mt genome and rRNA operon of two species of Diplostomum provide a valuable resource for novel genetic markers for species delineation and

  8. Epidemiological characterization of a nosocomial outbreak of extended spectrum β-lactamase Escherichia coli ST-131 confirms the clinical value of core genome multilocus sequence typing.

    PubMed

    Woksepp, Hanna; Ryberg, Anna; Berglind, Linda; Schön, Thomas; Söderman, Jan

    2017-09-28

    Enhanced precision of epidemiological typing in clinically suspected nosocomial outbreaks is crucial. Our aim was to investigate whether single nucleotide polymorphism (SNP) analysis and core genome (cg) multilocus sequence typing (MLST) of whole genome sequencing (WGS) data would more reliably identify a nosocomial outbreak, compared to earlier molecular typing methods. Sixteen isolates from a nosocomial outbreak of ESBL E. coli ST-131 in southeastern Sweden and three control strains were subjected to WGS. Sequences were explored by SNP analysis and cgMLST. cgMLST clearly differentiated between the outbreak isolates and the control isolates (>1400 differences). All clinically identified outbreak isolates showed close clustering (≥2 allele differences), except for two isolates (>50 allele differences). These data confirmed that the isolates with >50 differing genes did not belong to the nosocomial outbreak. The number of SNPs within the outbreak was ≤7, whereas the two discrepant isolates had >700 SNPs. Two of the ESBL E. coli ST-131 isolates did not belong to the clinically identified outbreak. Our results illustrate the power of WGS in terms of resolution, which may avoid overestimation of patients belonging to outbreaks as judged from epidemiological data and previously employed molecular methods with lower discriminatory ability. © 2017 APMIS. Published by John Wiley & Sons Ltd.

  9. Microsatellite DNA analysis revealed a drastic genetic change of Plasmodium vivax population in the Republic of Korea during 2002 and 2003.

    PubMed

    Iwagami, Moritoshi; Hwang, Seung-Young; Kim, So-Hee; Park, So-Jung; Lee, Ga-Young; Matsumoto-Takahashi, Emilie Louise Akiko; Kho, Weon-Gyu; Kano, Shigeyuki

    2013-01-01

    Vivax malaria was successfully eliminated in the Republic of Korea (South Korea) in the late 1970s, but it was found to have re-emerged from 1993. In order to control malaria and evaluate the effectiveness of malaria controls, it is important to develop a spatiotemporal understanding of the genetic structure of the parasite population. Here, we estimated the population structure and temporal dynamics of the transmission of Plasmodium vivax in South Korea by analyzing microsatellite DNA markers of the parasite. We analyzed 14 microsatellite DNA loci of the P. vivax genome from 163 South Korean isolates collected from 1994 to 2008. Allelic data were used to analyze linkage disequilibrium (LD), genetic differentiation and population structure, in order to make a detailed estimate of temporal change in the parasite population. The LD analysis showed a gradual decrease in LD levels, while the levels of genetic differentiation between successive years and analysis of the population structure based on the Bayesian approach suggested that a drastic genetic change occurred in the South Korean population during 2002 and 2003. Although relapse and asymptomatic parasite carriage might influence the population structure to some extent, our results suggested the continual introduction of P. vivax into South Korea through other parasite population sources. One possible source, particularly during 2002 and 2003, is North Korea. Molecular epidemiology using microsatellite DNA of the P. vivax population is effective for assessing the population structure and temporal dynamics of parasite transmission; information that can assist in the elimination of vivax malaria in endemic areas.

  10. High-quality draft genome sequence of Flavobacterium suncheonense GH29-5(T) (DSM 17707(T)) isolated from greenhouse soil in South Korea, and emended description of Flavobacterium suncheonense GH29-5(T).

    PubMed

    Tashkandy, Nisreen; Sabban, Sari; Fakieh, Mohammad; Meier-Kolthoff, Jan P; Huang, Sixing; Tindall, Brian J; Rohde, Manfred; Baeshen, Mohammed N; Baeshen, Nabih A; Lapidus, Alla; Copeland, Alex; Pillay, Manoj; Reddy, T B K; Huntemann, Marcel; Pati, Amrita; Ivanova, Natalia; Markowitz, Victor; Woyke, Tanja; Göker, Markus; Klenk, Hans-Peter; Kyrpides, Nikos C; Hahnke, Richard L

    2016-01-01

    Flavobacterium suncheonense is a member of the family Flavobacteriaceae in the phylum Bacteroidetes. Strain GH29-5(T) (DSM 17707(T)) was isolated from greenhouse soil in Suncheon, South Korea. F. suncheonense GH29-5(T) is part of the G enomic E ncyclopedia of B acteria and A rchaea project. The 2,880,663 bp long draft genome consists of 54 scaffolds with 2739 protein-coding genes and 82 RNA genes. The genome of strain GH29-5(T) has 117 genes encoding peptidases but a small number of genes encoding carbohydrate active enzymes (51 CAZymes). Metallo and serine peptidases were found most frequently. Among CAZymes, eight glycoside hydrolase families, nine glycosyl transferase families, two carbohydrate binding module families and four carbohydrate esterase families were identified. Suprisingly, polysaccharides utilization loci (PULs) were not found in strain GH29-5(T). Based on the coherent physiological and genomic characteristics we suggest that F. suncheonense GH29-5(T) feeds rather on proteins than saccharides and lipids.

  11. Molecular epidemiology of Staphylococcus aureus bacteremia in a single large Minnesota medical center in 2015 as assessed using MLST, core genome MLST and spa typing.

    PubMed

    Park, Kyung-Hwa; Greenwood-Quaintance, Kerryl E; Uhl, James R; Cunningham, Scott A; Chia, Nicholas; Jeraldo, Patricio R; Sampathkumar, Priya; Nelson, Heidi; Patel, Robin

    2017-01-01

    Staphylococcus aureus is a leading cause of bacteremia in hospitalized patients. Whether or not S. aureus bacteremia (SAB) is associated with clonality, implicating potential nosocomial transmission, has not, however, been investigated. Herein, we examined the epidemiology of SAB using whole genome sequencing (WGS). 152 SAB isolates collected over the course of 2015 at a single large Minnesota medical center were studied. Staphylococcus protein A (spa) typing was performed by PCR/Sanger sequencing; multilocus sequence typing (MLST) and core genome MLST (cgMLST) were determined by WGS. Forty-eight isolates (32%) were methicillin-resistant S. aureus (MRSA). The isolates encompassed 66 spa types, clustered into 11 spa clonal complexes (CCs) and 10 singleton types. 88% of 48 MRSA isolates belonged to spa CC-002 or -008. Methicillin-susceptible S. aureus (MSSA) isolates were more genotypically diverse, with 61% distributed across four spa CCs (CC-002, CC-012, CC-008 and CC-084). By MLST, there was 31 sequence types (STs), including 18 divided into 6 CCs and 13 singleton STs. Amongst MSSA isolates, the common MLST clones were CC5 (23%), CC30 (19%), CC8 (15%) and CC15 (11%). Common MRSA clones were CC5 (67%) and CC8 (25%); there were no MRSA isolates in CC45 or CC30. By cgMLST analysis, there were 9 allelic differences between two isolates, with the remaining 150 isolates differing from each other by over 40 alleles. The two isolates were retroactively epidemiologically linked by medical record review. Overall, cgMLST analysis resulted in higher resolution epidemiological typing than did multilocus sequence or spa typing.

  12. Molecular epidemiology of Staphylococcus aureus bacteremia in a single large Minnesota medical center in 2015 as assessed using MLST, core genome MLST and spa typing

    PubMed Central

    Park, Kyung-Hwa; Greenwood-Quaintance, Kerryl E.; Uhl, James R.; Cunningham, Scott A.; Chia, Nicholas; Jeraldo, Patricio R.; Sampathkumar, Priya; Nelson, Heidi

    2017-01-01

    Staphylococcus aureus is a leading cause of bacteremia in hospitalized patients. Whether or not S. aureus bacteremia (SAB) is associated with clonality, implicating potential nosocomial transmission, has not, however, been investigated. Herein, we examined the epidemiology of SAB using whole genome sequencing (WGS). 152 SAB isolates collected over the course of 2015 at a single large Minnesota medical center were studied. Staphylococcus protein A (spa) typing was performed by PCR/Sanger sequencing; multilocus sequence typing (MLST) and core genome MLST (cgMLST) were determined by WGS. Forty-eight isolates (32%) were methicillin–resistant S. aureus (MRSA). The isolates encompassed 66 spa types, clustered into 11 spa clonal complexes (CCs) and 10 singleton types. 88% of 48 MRSA isolates belonged to spa CC-002 or -008. Methicillin-susceptible S. aureus (MSSA) isolates were more genotypically diverse, with 61% distributed across four spa CCs (CC-002, CC-012, CC-008 and CC-084). By MLST, there was 31 sequence types (STs), including 18 divided into 6 CCs and 13 singleton STs. Amongst MSSA isolates, the common MLST clones were CC5 (23%), CC30 (19%), CC8 (15%) and CC15 (11%). Common MRSA clones were CC5 (67%) and CC8 (25%); there were no MRSA isolates in CC45 or CC30. By cgMLST analysis, there were 9 allelic differences between two isolates, with the remaining 150 isolates differing from each other by over 40 alleles. The two isolates were retroactively epidemiologically linked by medical record review. Overall, cgMLST analysis resulted in higher resolution epidemiological typing than did multilocus sequence or spa typing. PMID:28575112

  13. Chromosomal variation and genome size support existence of cryptic species of Triatoma dimidiata with different epidemiological importance as Chagas disease vectors.

    PubMed

    Panzera, F; Ferrandis, I; Ramsey, J; Ordòñez, R; Salazar-Schettino, P M; Cabrera, M; Monroy, M C; Bargues, M D; Mas-Coma, S; O'Connor, J E; Angulo, V M; Jaramillo, N; Cordón-Rosales, C; Gómez, D; Pérez, R

    2006-07-01

    The wide geographical distribution of Triatoma dimidiata, one of the three major vectors of Chagas disease, ranges from Mexico to northern Peru. Since this species occupies a great diversity of artificial and natural ecotopes, its eradication is extremely difficult. In order to assist control efforts, we used chromosome analyses and DNA amount as taxonomic markers to study genetic variability in populations of T. dimidiata from Mexico, Guatemala, El Salvador and Colombia. We differentiated three groups or cytotypes defined by characteristic chromosome C-banding patterns and genome size measured by flow cytometry. The three cytotypes are restricted to different geographic locations. Cytotype 1 occurs in Mexico (excluding Yucatán), Guatemala (excluding Petén), El Salvador and Colombia. Cytotype 2 occurs in Yucatán and cytotype 3 occurs in Petén. Cytotype 1, commonly associated with domestic and peridomestic environments but also inhabiting sylvatic ecotopes, is the most widespread and with major epidemiological significance. In contrast, the Yucatán cytotype inhabits wild ecotopes but increasingly enters houses, while the Petén cytotype appears exclusively sylvatic. We suggest that these cytotypes represent cryptic species of T. dimidiata with different epidemiological relevance as Chagas disease vectors. Poor ability to colonize human dwellings, together with their restricted geographic distribution, indicate that the Yucatán and Petén putative species probably have much less epidemiological significance than cytotype 1. Thus, the genetic markers we describe are powerful tools to differentiate cryptic species in T. dimidiata with different epidemiological significance, contributing to planning the most effective control measures.

  14. The EU FP6 EpiGenChlamydia Consortium: contribution of molecular epidemiology and host-pathogen genomics to understanding Chlamydia trachomatis-related disease.

    PubMed

    Morré, S A; Ouburg, S; Peña, A S; Brand, A

    2009-11-01

    Chlamydia trachomatis infections are responsible for the world's leading cause of blindness (trachoma) and its most prevalent sexually transmitted disease, which is strongly associated with pelvic inflammatory disease, ectopic pregnancy and tubal infertility. Twin study-based findings of members of EpiGenChlamydia Consortium estimate that there is a 40% genetic predisposition to C. trachomatis infections. It is likely that the advances in human genomics will help to unravel the genetic predisposition at the gene level and will help to define a genetic fingerprint that can be used as a marker for this predisposition. The information gathered to date suggests that this predisposition and the factors contributing to prognosis are multifactorial. The EpiGenChlamydia Consortium aims to structure transnational research to such a degree that comparative genomics and genetic epidemiology can be performed in large numbers of unrelated individuals. Biobanking and data-warehouse building are the most central deliverables of the Coordination Action of the Consortium in Functional Genomics Research. In addition, the collective synergy acquired in this Coordination Action will allow for the generation of scientific knowledge on the C. trachomatis-host interaction, knowledge on the genetic predisposition to C. trachomatis infection and the development of tools for early detection of a predisposition to C. trachomatis infection and its complications. This review summarizes the consortium aims and progress, and future perspectives and directions.

  15. Epidemiology of Childhood Obesity in Korea

    PubMed Central

    2016-01-01

    Over the past several decades, the prevalence of obesity has increased dramatically worldwide and is increasing not only in developed countries, but also in developing countries. This increase may lead to an increase in the incidence of chronic diseases throughout the lifespan. In Korean children and adolescents, the prevalence of obesity increased from 6.8% in 1998 to 10.0% in 2013. Obesity is a state that more commonly influences children and adolescents of lower socioeconomic status (SES) than those with a higher SES. However, the prevalence of metabolic syndrome in a nationally representative sample of Korean adolescents decreased from 1998 to 2012. According to the Diabetes Fact Sheet of the Korean Diabetes Association, the prevalence of type 2 diabetes among children aged 18 years or younger was 153.5 per 100,000 in 2006 and 205.0 per 100,000 in 2013. Obesity is a complex disease influenced by many interacting factors, such as adipocytokines, lipopolysaccharide-binding protein, adenovirus 36 infection, birth weight, lifestyle, and endocrine-disrupting chemicals. Obesity in youth can adversely impact practically every organ system and lead to serious consequences, such as metabolic, gastrointestinal, pulmonary, cardiovascular, and psychosocial complications. Therefore, coordinated efforts by governments, organizations, communities, and individuals are needed to prevent and treat childhood obesity. In particular, a long-term policy to improve the social environment will also be necessary. PMID:27834078

  16. 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.

  17. 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

  18. 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

  19. Comparative evaluation of use of cna, fnbA, fnbB, and hlb for genomic fingerprinting in the epidemiological typing of Staphylococcus aureus.

    PubMed

    Smeltzer, M S; Gillaspy, A F; Pratt, F L; Thames, M D

    1997-10-01

    We used a genomic fingerprinting protocol to characterize 59 Staphylococcus aureus strains and a single S. intermedius isolate, all of which were previously typed by 13 different methods (F. C. Tenover et al., J. Clin. Microbiol. 32:407-415, 1994). These 60 strains were divided into three groups of 20 strains each, with each group including internal controls. Two of the three groups (groups SB and SC) included 29 strains from four relatively well-defined outbreaks. The epidemiological relationships of the strains in the third group (group SA) were unclear. Fingerprints were established by Southern blotting with HaeIII-digested genomic DNA and a probe mixture consisting of DNA fragments corresponding to the S. aureus collagen adhesin (cna), fibronectin-binding protein (fnbA and fnbB), and beta-toxin (hlb) genes. An unambiguous fingerprint was obtained for all S. aureus isolates. No hybridization signal was observed with S. intermedius. Twenty-seven of the 29 related strains in the SB and SC groups were correctly identified as belonging to one of the four epidemiologically related groups. Our protocol was less successful with respect to the exclusion of unrelated strains. Specifically, only 6 of 11 unrelated strains in the SB and SC groups had a fingerprint that was distinct by comparison to the fingerprints of the outbreak strains. Nevertheless, our protocol was relatively accurate by comparison to the accuracies of the other methods and was one of only six methods that accurately identified all of the repetitive strains included as internal controls.

  20. Evaluation of Whole Genome Mapping as a Fast and Automated Molecular Epidemiological Tool for the Study of Cronobacter spp. in Powdered Infant Formula Processing Facilities.

    PubMed

    Tang, Yanjie; Rasschaert, Geertrui; Yu, Liping; Chilton, Claire; Baert, Leen

    2017-09-01

    Cronobacter has been identified as the causative agent of outbreaks or sporadic cases of meningitis, necrotizing enterocolitis, and septicemia associated with powdered infant formula. Food processing environments may provide a possible contamination route. The purpose of this study was to evaluate whole genome mapping (WGM) as a fast and automated molecular epidemiological method for characterizing Cronobacter spp. in the processing environment. This is the first study indicating the applicability of WGM to Cronobacter. WGM was compared with ribotyping, which is often used as an automated typing tool, and with pulsed-field gel electrophoresis, which is a well-known and highly discriminating tool that is also based on restriction site analysis. The comparison of the three tools was carried out on a subset of Cronobacter isolates collected from 2011 to 2014 through a monitoring program. The performance characteristics of WGM have not yet been described; therefore, in the current study its performance was evaluated based on five criteria: typeability, reproducibility, stability, epidemiological concordance, and the discrimination power. WGM was shown to produce typeable, reproducible, and stable results. With a similar cut-off of 98%, WGM was shown to have a discriminatory power equivalent to pulsed-field gel electrophoresis and higher than ribotyping. Future studies are needed to confirm the indicated cut-off level of 98%.

  1. Whole Genome Sequencing-Based Molecular Epidemiologic Analysis of Autochthonous Dengue Virus Type 1 Strains Circulating in Japan in 2014.

    PubMed

    Tajima, Shigeru; Nakayama, Eri; Kotaki, Akira; Moi, Meng Ling; Ikeda, Makiko; Yagasaki, Kazumi; Saito, Yuka; Shibasaki, Ken-Ichi; Saijo, Masayuki; Takasaki, Tomohiko

    2017-01-24

    Cases of autochthonous infections of dengue virus type 1 (DENV-1) were detected in Japan after a 70-year period devoid of dengue outbreaks. We previously showed that E gene sequences are identical in 11 of the 12 DENV-1 strains autochthonous to Japan. However, the E sequence represents only 14% of the DENV-1 genome. In the present study, we have sequenced the entire genome of 6 autochthonous DENV-1 strains that were isolated from patients during the 2014 outbreak. Sequencing of 5 Yoyogi group strains with identical E sequences and 1 Shizuoka strain with a different E sequence revealed that the first Yoyogi group strain differed from the Shizuoka strain by 18 amino acid residues. Furthermore, 2 Yoyogi group strains had different genomic sequences while the other 3 had identical genomes. Phylogenetic analyses indicated that the Hyogo strain, a Yoyogi group strain, was the first to diverge from the other 4 Yoyogi group strains. The E gene sequence of the Yoyogi group strains exhibits the highest homology to those of the strains isolated in Malaysia and Singapore between 2013 and 2014. The patient infected with the Hyogo strain visited Malaysia before the onset of dengue fever, suggesting that this was a case of dengue infection imported from Malaysia.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. Towards an integrated food safety surveillance system: a simulation study to explore the potential of combining genomic and epidemiological metadata

    PubMed Central

    Crotta, M.; Wall, B.; Good, L.; O'Brien, S. J.; Guitian, J.

    2017-01-01

    Foodborne infection is a result of exposure to complex, dynamic food systems. The efficiency of foodborne infection is driven by ongoing shifts in genetic machinery. Next-generation sequencing technologies can provide high-fidelity data about the genetics of a pathogen. However, food safety surveillance systems do not currently provide similar high-fidelity epidemiological metadata to associate with genetic data. As a consequence, it is rarely possible to transform genetic data into actionable knowledge that can be used to genuinely inform risk assessment or prevent outbreaks. Big data approaches are touted as a revolution in decision support, and pose a potentially attractive method for closing the gap between the fidelity of genetic and epidemiological metadata for food safety surveillance. We therefore developed a simple food chain model to investigate the potential benefits of combining ‘big’ data sources, including both genetic and high-fidelity epidemiological metadata. Our results suggest that, as for any surveillance system, the collected data must be relevant and characterize the important dynamics of a system if we are to properly understand risk: this suggests the need to carefully consider data curation, rather than the more ambitious claims of big data proponents that unstructured and unrelated data sources can be combined to generate consistent insight. Of interest is that the biggest influencers of foodborne infection risk were contamination load and processing temperature, not genotype. This suggests that understanding food chain dynamics would probably more effectively generate insight into foodborne risk than prescribing the hazard in ever more detail in terms of genotype. PMID:28405360

  7. Towards an integrated food safety surveillance system: a simulation study to explore the potential of combining genomic and epidemiological metadata.

    PubMed

    Hill, A A; Crotta, M; Wall, B; Good, L; O'Brien, S J; Guitian, J

    2017-03-01

    Foodborne infection is a result of exposure to complex, dynamic food systems. The efficiency of foodborne infection is driven by ongoing shifts in genetic machinery. Next-generation sequencing technologies can provide high-fidelity data about the genetics of a pathogen. However, food safety surveillance systems do not currently provide similar high-fidelity epidemiological metadata to associate with genetic data. As a consequence, it is rarely possible to transform genetic data into actionable knowledge that can be used to genuinely inform risk assessment or prevent outbreaks. Big data approaches are touted as a revolution in decision support, and pose a potentially attractive method for closing the gap between the fidelity of genetic and epidemiological metadata for food safety surveillance. We therefore developed a simple food chain model to investigate the potential benefits of combining 'big' data sources, including both genetic and high-fidelity epidemiological metadata. Our results suggest that, as for any surveillance system, the collected data must be relevant and characterize the important dynamics of a system if we are to properly understand risk: this suggests the need to carefully consider data curation, rather than the more ambitious claims of big data proponents that unstructured and unrelated data sources can be combined to generate consistent insight. Of interest is that the biggest influencers of foodborne infection risk were contamination load and processing temperature, not genotype. This suggests that understanding food chain dynamics would probably more effectively generate insight into foodborne risk than prescribing the hazard in ever more detail in terms of genotype.

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

    DOE PAGES

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

    2016-03-07

    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 ofmore » 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

  9. 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

  10. 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

  11. Genomic epidemiology of Cryptococcus yeasts identifies adaptation to environmental niches underpinning infection across an African HIV/AIDS cohort.

    PubMed

    Vanhove, Mathieu; Beale, Mathew A; Rhodes, Johanna; Chanda, Duncan; Lakhi, Shabir; Kwenda, Geoffrey; Molloy, Sile; Karunaharan, Natasha; Stone, Neil; Harrison, Thomas S; Bicanic, Tihana; Fisher, Matthew C

    2017-04-01

    Emerging infections caused by fungi have become a widely recognized global phenomenon and are causing an increasing burden of disease. Genomic techniques are providing new insights into the structure of fungal populations, revealing hitherto undescribed fine-scale adaptations to environments and hosts that govern their emergence as infections. Cryptococcal meningitis is a neglected tropical disease that is responsible for a large proportion of AIDS-related deaths across Africa; however, the ecological determinants that underlie a patient's risk of infection remain largely unexplored. Here, we use genome sequencing and ecological genomics to decipher the evolutionary ecology of the aetiological agents of cryptococcal meningitis, Cryptococcus neoformans and Cryptococcus gattii, across the central African country of Zambia. We show that the occurrence of these two pathogens is differentially associated with biotic (macroecological) and abiotic (physical) factors across two key African ecoregions, Central Miombo woodlands and Zambezi Mopane woodlands. We show that speciation of Cryptococcus has resulted in adaptation to occupy different ecological niches, with C. neoformans found to occupy Zambezi Mopane woodlands and C. gattii primarily recovered from Central Miombo woodlands. Genome sequencing shows that C. neoformans causes 95% of human infections in this region, of which over three-quarters belonged to the globalized lineage VNI. We show that VNI infections are largely associated with urbanized populations in Zambia. Conversely, the majority of C. neoformans isolates recovered in the environment belong to the genetically diverse African-endemic lineage VNB, and we show hitherto unmapped levels of genomic diversity within this lineage. Our results reveal the complex evolutionary ecology that underpins the reservoirs of infection for this, and likely other, deadly pathogenic fungi. © 2016 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

  12. Invited Commentary: Integrating Genomics and Social Epidemiology-Analysis of Late-Life Low Socioeconomic Status and the Conserved Transcriptional Response to Adversity.

    PubMed

    Belsky, Daniel W; Snyder-Mackler, Noah

    2017-09-01

    Socially disadvantaged children face increased morbidity and mortality as they age. Understanding mechanisms through which social disadvantage becomes biologically embedded and devising measurements that can track this embedding are critical priorities for research to address social gradients in health. The analysis by Levine et al. (Am J Epidemiol. 2017;186(5):503-509) of genome-wide gene expression in a subsample of US Health and Retirement Study participants suggests important new directions for the field. Specifically, findings suggest promise in integrating gene expression data into population studies and provide further evidence for the conserved transcriptional response to adversity as a marker of biological embedding of social disadvantage. The study also highlights methodological issues related to the analysis of gene expression data and social gradients in health and a need to examine the conserved transcriptional response to adversity alongside other proposed measurements of biological embedding. Looking to the future, advances in genome science are opening new opportunities for sociogenomic epidemiology. © The Author(s) 2017. Published by Oxford University Press on behalf of the Johns Hopkins Bloomberg School of Public Health. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  13. Regional Disease Vector Ecology Profile: The Koreas

    DTIC Science & Technology

    2015-01-01

    Epidemiology: Tick-borne Encephalitis (TBE) is a zoonotic viral infectious disease involving the central nervous system . In humans, the disease most...subsequently enter and multiply in the circulatory system of the louse. Lice are highly infective after 6 days and remain so for life (30-40 days...Regional Disease Vector Ecology Profile: The Koreas Published and Distributed by the Armed Forces Pest Management Board Information

  14. Detection of Multiple Parallel Transmission Outbreak of Streptococcus suis Human Infection by Use of Genome Epidemiology, China, 2005

    PubMed Central

    Du, Pengcheng; Zheng, Han; Zhou, Jieping; Lan, Ruiting; Ye, Changyun; Jing, Huaiqi; Jin, Dong; Cui, Zhigang; Bai, Xuemei; Liang, Jianming; Liu, Jiantao; Xu, Lei; Zhang, Wen; Chen, Chen

    2017-01-01

    Streptococcus suis sequence type 7 emerged and caused 2 of the largest human infection outbreaks in China in 1998 and 2005. To determine the major risk factors and source of the infections, we analyzed whole genomes of 95 outbreak-associated isolates, identified 160 single nucleotide polymorphisms, and classified them into 6 clades. Molecular clock analysis revealed that clade 1 (responsible for the 1998 outbreak) emerged in October 1997. Clades 2–6 (responsible for the 2005 outbreak) emerged separately during February 2002–August 2004. A total of 41 lineages of S. suis emerged by the end of 2004 and rapidly expanded to 68 genome types through single base mutations when the outbreak occurred in June 2005. We identified 32 identical isolates and classified them into 8 groups, which were distributed in a large geographic area with no transmission link. These findings suggest that persons were infected in parallel in respective geographic sites. PMID:27997331

  15. Complete Genome Sequence of Klebsiella pneumoniae subsp. pneumoniae KP617, Coproducing OXA-232 and NDM-1 Carbapenemases, Isolated in South Korea

    PubMed Central

    Kwon, Taesoo; Yang, Ji Woo; Lee, Sanghyun; Yun, Mi-ran; Yoo, Won Gi; Kim, Hwa Su

    2016-01-01

    The prevalence of Klebsiella pneumoniae coproducing carbapenemase metallo-β-lactamase 1 (NDM-1) and OXA-48 has been increasing globally since 2013. The complete genome of KP617 was sequenced and assembled into a circular chromosome and two plasmids. This sequence provides the genetic background for understanding the evolution of carbapenemase genes in K. pneumoniae KP617. PMID:26769936

  16. Draft genome sequence of the fungus associated with oak-wilt mortality in South Korea, Raffaelea quercus-mongolicae KACC44405

    Treesearch

    Jongbum Jeon; Ki-Tae Kim; Hyeunjeong Song; Gir-Won Lee; Kyeongchae Cheong; Hyunbin Kim; Gobong Choi; Yong-Hwan Lee; Jane E. Stewart; Ned B. Klopfenstein; Mee-Sook Kim

    2017-01-01

    The fungus Raffaelea quercus-mongolicae is the causal agent of Korean oak wilt, a disease associated with mass mortality of oak trees (e.g., Quercus spp.). The fungus is vectored and dispersed by the ambrosia beetle, Platypus koryoensis. Here, we present the 27.0-Mb draft genome sequence of R. quercus-mongolicae strain KACC44405.

  17. Draft Genome Sequence of Fusobacterium nucleatum subsp. vincentii ChDC F8, Isolated from a Human Subgingival Plaque in the Republic of Korea

    PubMed Central

    Park, Soon-Nang; Cho, Eugene; Kim, Hwa-Sook; Kim, Dae-Soo; Jung, Jaeeun; Baek, Jeong-Hun; Kyong Lim, Yun; Jo, Eojin; Chang, Young-Hyo; Hwan Shin, Jeong; Kim, Jihun; Choi, Sang-Haeng; Kang, Jihee; Choi, YongUn; Park, Hong-Seog; Kim, Hongik

    2013-01-01

    Fusobacterium nucleatum is a Gram-negative, nonmotile, obligately anaerobic rod bacterium which might play an important role in the initiation and progression of periodontal diseases. F. nucleatum subsp. vincentii ChDC F8 (KCOM 1231) was isolated from a human gingivitis lesion. Here, we report the draft genome sequence of the strain. PMID:24336378

  18. Draft Genome Sequence of Fusobacterium nucleatum subsp. nucleatum ChDC F316, Isolated from a Human Peri-implantitis Lesion in the Republic of Korea

    PubMed Central

    Park, Soon-Nang; Cho, Eugene; Kim, Hwa-Sook; Kim, Dae-Soo; Jung, Jaeeun; Baek, Jeong-Hun; Kyong Lim, Yun; Jo, Eojin; Chang, Young-Hyo; Hwan Shin, Jeong; Choi, Sang-Haeng; Kang, Jihee; Choi, YongUn; Park, Hong-Seog; Kim, Hongik

    2013-01-01

    Fusobacterium nucleatum is a Gram-negative anaerobe and is one of the causative agents of periodontal diseases, including peri-implantitis. Fusobacterium nucleatum subsp. nucleatum ChDC F316 (KCOM 1322) was isolated from a human peri-implantitis lesion. Here, we report the draft genome sequence of this strain. PMID:24336379

  19. Complete Genome Sequence of Human Adenovirus Type 55 Associated with Acute Respiratory Disease, Isolated from a Military Base in the Republic of Korea

    PubMed Central

    Gu, Se Hun; Song, Dong Hyun; Lee, Daesang; Huh, Kyungmin; Yoo, Hongseok; Oh, Hong Sang; Jung, Jaehun; Woo, Koung In; Kim, Mirang; Seog, Woong; Hwang, Il-Ung

    2017-01-01

    ABSTRACT Human adenovirus (HAdV) (genus Mastadenovirus; family Adenoviridae) serotype 55 is a reemerging pathogen associated with acute respiratory disease. Here, we report the complete genome sequence of HAdV-55 strain AFMC 16-0011, isolated from a military recruit, using next-generation sequencing technology. PMID:28280019

  20. Nation Building in Korea

    DTIC Science & Technology

    1995-04-01

    opportunity to rebuild South Korea . He saw it as “something almost unique in history. It is the opportunity of an army in a foreign land to contribute...problems. The North Korean invasion in 1950 wedded South Korea to the United States and confronted the United States with the enormous task of...elections in Korea .8 After failing to achieve agreement to peninsula-wide elections, the United Nations sponsored elections in South

  1. Complete Genome and Molecular Epidemiological Data Infer the Maintenance of Rabies among Kudu (Tragelaphus strepsiceros) in Namibia

    PubMed Central

    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

  2. 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.

  3. 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

  4. Molecular Epidemiology and Genome Dynamics of New Delhi Metallo-β-Lactamase-Producing Extraintestinal Pathogenic Escherichia coli Strains from India

    PubMed Central

    Ranjan, Amit; Shaik, Sabiha; Mondal, Agnismita; Nandanwar, Nishant; Hussain, Arif; Semmler, Torsten; Kumar, Narender; Tiwari, Sumeet K.; Jadhav, Savita; Wieler, Lothar H.

    2016-01-01

    The global dissemination and increasing incidence of carbapenem-resistant, Gram-negative organisms have resulted in acute public health concerns. Here, we present a retrospective multicenter study on molecular characterization of metallo-β-lactamase (MBL)-producing clinical Escherichia coli isolates recovered from extraintestinal infections in two hospitals in Pune, India. We screened a large sample size of 510 E. coli isolates for MBL production wherein we profiled their molecular determinants, antimicrobial resistance phenotypes, functional virulence properties, genomic features, and transmission dynamics. Approximately 8% of these isolates were MBL producers, the majority of which were of the NDM-1 (69%) type, followed by NDM-5 (19%), NDM-4 (5.5%), and NDM-7 (5.5%). MBL producers were resistant to all antibiotics tested except for colistin, fosfomycin, and chloramphenicol, which were effective to various extents. Plasmids were found to be an effective means of dissemination of NDM genes and other resistance traits. All MBL producers adhered to and invaded bladder epithelial (T24) cells and demonstrated significant serum resistance. Genomic analysis of MBL-producing E. coli isolates revealed higher resistance but a moderate virulence gene repertoire. A subset of NDM-1-positive E. coli isolates was identified as dominant sequence type 101 (ST101) while two strains belonging to ST167 and ST405 harbored NDM-5. A majority of MBL-producing E. coli strains revealed unique genotypes, suggesting that they were clonally unrelated. Overall, the coexistence of virulence and carbapenem resistance in clinical E. coli isolates is of serious concern. Moreover, the emergence of NDM-1 among the globally dominant E. coli ST101 isolates warrants stringent surveillance and control measures. PMID:27600040

  5. Associations Between Incident Ischemic Stroke Events and Stroke and Cardiovascular Disease-Related GWAS SNPs in the Population Architecture Using Genomics and Epidemiology (PAGE) Study

    PubMed Central

    Carty, Cara L.; Bůžková, Petra; Fornage, Myriam; Franceschini, Nora; Cole, Shelley; Heiss, Gerardo; Hindorff, Lucia A.; Howard, Barbara V.; Mann, Sue; Martin, Lisa W.; Zhang, Ying; Matise, Tara C.; Prentice, Ross; Reiner, Alexander P.; Kooperberg, Charles

    2012-01-01

    Background Genome-wide association studies (GWAS) have identified loci associated with ischemic stroke (IS) and cardiovascular disease (CVD) in European-descent individuals, but their replication in different populations has been largely unexplored. Methods and Results Nine single-nucleotide polymorphisms (SNPs) selected from GWAS and meta-analyses of stroke and 86 SNPs previously associated with myocardial infarction and CVD risk factors including blood lipids (HDL, LDL, triglycerides), type 2 diabetes and body mass index were investigated for associations with incident IS in European Americans (EA) N=26,276; African Americans (AA) N=8970; and American Indians (AI) N= 3570 from the Population Architecture using Genomics and Epidemiology Study. Ancestry-specific fixed effects meta-analysis with inverse variance weighting was used to combine study-specific log hazard ratios from Cox proportional hazards models. Two of 9 stroke SNPs (rs783396 and rs1804689) were associated with increased IS hazard in AA; none were significant in this large EA cohort. Of 73 CVD risk factor SNPs tested in EA, two (HDL and triglycerides SNPs) were associated with IS. In AA, SNPs associated with LDL, HDL and BMI were significantly associated with IS (3 of 86 SNPs tested). Out of 58 SNPs tested in AI, one LDL SNP was significantly associated with IS. Conclusions Our analyses showing lack of replication in spite of reasonable power for many stroke SNPs and differing results by ancestry highlight the need to follow-up on GWAS findings and conduct genetic association studies in diverse populations. We found modest IS associations with BMI and lipids SNPs, though these findings require confirmation. PMID:22403240

  6. 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.

  7. Analysis of metabolic syndrome components in >15 000 african americans identifies pleiotropic variants: results from the population architecture using genomics and epidemiology study.

    PubMed

    Carty, Cara L; Bhattacharjee, Samsiddhi; Haessler, Jeff; Cheng, Iona; Hindorff, Lucia A; Aroda, Vanita; Carlson, Christopher S; Hsu, Chun-Nan; Wilkens, Lynne; Liu, Simin; Selvin, Elizabeth; Jackson, Rebecca; North, Kari E; Peters, Ulrike; Pankow, James S; Chatterjee, Nilanjan; Kooperberg, Charles

    2014-08-01

    Metabolic syndrome (MetS) refers to the clustering of cardiometabolic risk factors, including dyslipidemia, central adiposity, hypertension, and hyperglycemia, in individuals. Identification of pleiotropic genetic factors associated with MetS traits may shed light on key pathways or mediators underlying MetS. Using the Metabochip array in 15 148 African Americans from the Population Architecture using Genomics and Epidemiology (PAGE) study, we identify susceptibility loci and investigate pleiotropy among genetic variants using a subset-based meta-analysis method, ASsociation-analysis-based-on-subSETs (ASSET). Unlike conventional models that lack power when associations for MetS components are null or have opposite effects, Association-analysis-based-on-subsets uses 1-sided tests to detect positive and negative associations for components separately and combines tests accounting for correlations among components. With Association-analysis-based-on-subsets, we identify 27 single nucleotide polymorphisms in 1 glucose and 4 lipids loci (TCF7L2, LPL, APOA5, CETP, and APOC1/APOE/TOMM40) significantly associated with MetS components overall, all P<2.5e-7, the Bonferroni adjusted P value. Three loci replicate in a Hispanic population, n=5172. A novel African American-specific variant, rs12721054/APOC1, and rs10096633/LPL are associated with ≥3 MetS components. We find additional evidence of pleiotropy for APOE, TOMM40, TCF7L2, and CETP variants, many with opposing effects (eg, the same rs7901695/TCF7L2 allele is associated with increased odds of high glucose and decreased odds of central adiposity). We highlight a method to increase power in large-scale genomic association analyses and report a novel variant associated with all MetS components in African Americans. We also identify pleiotropic associations that may be clinically useful in patient risk profiling and for informing translational research of potential gene targets and medications. © 2014 American Heart

  8. 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

  9. Resurgence of Mumps in Korea

    PubMed Central

    2015-01-01

    Routine vaccination against mumps has markedly reduced its incidence. However, the incidence of mumps continuously has increased since 2007. In 2013, a large mumps epidemic occurred in Korea, and this epidemic is still an ongoing problem. This epidemic occurred primarily in school settings and affected vaccinated adolescents, predominantly male students. The recent resurgence of mumps is caused by multiple factors: suboptimal effectiveness of the current mumps vaccines, use of the Rubini strain vaccine, waning immunity in the absence of natural boosting due to the marked reduction in the mumps incidence, genotype mismatch between the vaccine and circulating mumps virus strains, and environmental conditions that foster intense exposures. Containment of mumps outbreaks is challenging because the sensitivity of diagnostic tests is low among vaccinees and control measures are less efficient because of the inherent nature of the mumps virus. Despite the suboptimal vaccine effectiveness in outbreak settings, maintaining the high vaccine coverage is an important strategy to prevent mumps outbreaks, given that the routine use of mumps vaccines has substantially reduced the incidence of mumps and its complications as compared with that in the pre-vaccine era. In order to control the current mumps epidemic and prevent further outbreaks, we need to better understand the dynamics of mumps among vaccinated populations and the changing epidemiology in Korea. Concerted efforts should be made to systematically monitor the immunization status of the Korean population and to improve diagnosis efficiency. Furthermore, more effective mumps vaccines need to be developed in the future. PMID:25844258

  10. 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).

  11. 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

    DOE PAGES

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

    2016-01-19

    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 phylogenymore » 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.« less

  12. 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

    SciTech Connect

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

    2016-01-19

    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.

  13. 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.

  14. 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)

  15. Investigation of gene-by-sex interactions for lipid traits in diverse populations from the population architecture using genomics and epidemiology study

    PubMed Central

    2013-01-01

    Background High-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), and triglyceride (TG) levels are influenced by both genes and the environment. Genome-wide association studies (GWAS) have identified ~100 common genetic variants associated with HDL-C, LDL-C, and/or TG levels, mostly in populations of European descent, but little is known about the modifiers of these associations. Here, we investigated whether GWAS-identified SNPs for lipid traits exhibited heterogeneity by sex in the Population Architecture using Genomics and Epidemiology (PAGE) study. Results A sex-stratified meta-analysis was performed for 49 GWAS-identified SNPs for fasting HDL-C, LDL-C, and ln(TG) levels among adults self-identified as European American (25,013). Heterogeneity by sex was established when phet < 0.001. There was evidence for heterogeneity by sex for two SNPs for ln(TG) in the APOA1/C3/A4/A5/BUD13 gene cluster: rs28927680 (phet = 7.4x10-7) and rs3135506 (phet = 4.3x10-4), one SNP in PLTP for HDL levels (rs7679; phet = 9.9x10-4), and one in HMGCR for LDL levels (rs12654264; phet = 3.1x10-5). We replicated heterogeneity by sex in five of seventeen loci previously reported by genome-wide studies (binomial p = 0.0009). We also present results for other racial/ethnic groups in the supplementary materials, to provide a resource for future meta-analyses. Conclusions We provide further evidence for sex-specific effects of SNPs in the APOA1/C3/A4/A5/BUD13 gene cluster, PLTP, and HMGCR on fasting triglyceride levels in European Americans from the PAGE study. Our findings emphasize the need for considering context-specific effects when interpreting genetic associations emerging from GWAS, and also highlight the difficulties in replicating interaction effects across studies and across racial/ethnic groups. PMID:23634756

  16. [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.

  17. Genetic epidemiology and genome-wide linkage analysis of carotid artery ultrasound traits in multigenerational African ancestry families.

    PubMed

    Kuipers, Allison L; Kammerer, Candace M; Miljkovic, Iva; Woodard, Genevieve A; Bunker, Clareann H; Patrick, Alan L; Wheeler, Victor W; Newman, Anne B; Zmuda, Joseph M

    2013-11-01

    Intima-media thickness, adventitial diameter and lumen diameter are indicators of cardiovascular disease risk. The influence of genetic factors on these measures in African ancestry populations is not well defined. Therefore, we estimated heritability and performed genome-wide linkage analysis of carotid ultrasound traits in 7 multigenerational families of African ancestry. A total of 395 individuals (7 pedigrees; mean family size = 56; 2392 relative pairs) aged ≥18 years had a common carotid artery ultrasound scan. Statistical analyses were conducted using pedigree-based maximum likelihood methods. Significant covariates included age, sex, body mass index or height and waist, and systolic blood pressure. Residual heritabilities ranged from 0.35 ± 0.10 to 0.64 ± 0.12 (P < 0.0001). We identified a novel quantitative trait locus for adventitial and lumen diameters on chromosome 11 (max LOD = 4.09, 133 cm). Further fine mapping of this region may identify specific mutations predisposing to subclinical vascular disease among African ancestry individuals. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  18. Generating testable hypotheses for schizophrenia and rheumatoid arthritis pathogenesis by integrating epidemiological, genomic, and protein interaction data.

    PubMed

    Malavia, Tulsi A; Chaparala, Srilakshmi; Wood, Joel; Chowdari, Kodavali; Prasad, Konasale M; McClain, Lora; Jegga, Anil G; Ganapathiraju, Madhavi K; Nimgaonkar, Vishwajit L

    2017-01-01

    Patients with schizophrenia and their relatives have reduced prevalence of rheumatoid arthritis. Schizophrenia and rheumatoid arthritis genome-wide association studies also indicate negative genetic correlations, suggesting that there may be shared pathogenesis at the DNA level or downstream. A portion of the inverse prevalence could be attributed to pleiotropy, i.e., variants of a single nucleotide polymorphism that could confer differential risk for these disorders. To study the basis for such an interrelationship, we initially compared lists of single nucleotide polymorphisms with significant genetic associations (p < 1(e-8)) for schizophrenia or rheumatoid arthritis, evaluating patterns of linkage disequilibrium and apparent pleiotropic risk profiles. Single nucleotide polymorphisms that conferred risk for both schizophrenia and rheumatoid arthritis were localized solely to the extended HLA region. Among single nucleotide polymorphisms that conferred differential risk for schizophrenia and rheumatoid arthritis, the majority were localized to HLA-B, TNXB, NOTCH4, HLA-C, HCP5, MICB, PSORS1C1, and C6orf10; published functional data indicate that HLA-B and HLA-C have the most plausible pathogenic roles in both disorders. Interactomes of these eight genes were constructed from protein-protein interaction information using publicly available databases and novel computational predictions. The genes harboring apparently pleiotropic single nucleotide polymorphisms are closely connected to rheumatoid arthritis and schizophrenia associated genes through common interacting partners. A separate and independent analysis of the interactomes of rheumatoid arthritis and schizophrenia genes showed a significant overlap between the two interactomes and that they share several common pathways, motivating functional studies suggesting a relationship in the pathogenesis of schizophrenia/rheumatoid arthritis.

  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. PMID:27682088

  20. A meta-analysis of four genome-wide association studies of survival to age 90 years or older: the Cohorts for Heart and Aging Research in Genomic Epidemiology Consortium.

    PubMed

    Newman, Anne B; Walter, Stefan; Lunetta, Kathryn L; Garcia, Melissa E; Slagboom, P Eline; Christensen, Kaare; Arnold, Alice M; Aspelund, Thor; Aulchenko, Yurii S; Benjamin, Emelia J; Christiansen, Lene; D'Agostino, Ralph B; Fitzpatrick, Annette L; Franceschini, Nora; Glazer, Nicole L; Gudnason, Vilmundur; Hofman, Albert; Kaplan, Robert; Karasik, David; Kelly-Hayes, Margaret; Kiel, Douglas P; Launer, Lenore J; Marciante, Kristin D; Massaro, Joseph M; Miljkovic, Iva; Nalls, Michael A; Hernandez, Dena; Psaty, Bruce M; Rivadeneira, Fernando; Rotter, Jerome; Seshadri, Sudha; Smith, Albert V; Taylor, Kent D; Tiemeier, Henning; Uh, Hae-Won; Uitterlinden, André G; Vaupel, James W; Walston, Jeremy; Westendorp, Rudi G J; Harris, Tamara B; Lumley, Thomas; van Duijn, Cornelia M; Murabito, Joanne M

    2010-05-01

    Genome-wide association studies (GWAS) may yield insights into longevity. We performed a meta-analysis of GWAS in Caucasians from four prospective cohort studies: the Age, Gene/Environment Susceptibility-Reykjavik Study, the Cardiovascular Health Study, the Framingham Heart Study, and the Rotterdam Study participating in the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium. Longevity was defined as survival to age 90 years or older (n = 1,836); the comparison group comprised cohort members who died between the ages of 55 and 80 years (n = 1,955). In a second discovery stage, additional genotyping was conducted in the Leiden Longevity Study cohort and the Danish 1905 cohort. There were 273 single-nucleotide polymorphism (SNP) associations with p < .0001, but none reached the prespecified significance level of 5 x 10(-8). Of the most significant SNPs, 24 were independent signals, and 16 of these SNPs were successfully genotyped in the second discovery stage, with one association for rs9664222, reaching 6.77 x 10(-7) for the combined meta-analysis of CHARGE and the stage 2 cohorts. The SNP lies in a region near MINPP1 (chromosome 10), a well-conserved gene involved in regulation of cellular proliferation. The minor allele was associated with lower odds of survival past age 90 (odds ratio = 0.82). Associations of interest in a homologue of the longevity assurance gene (LASS3) and PAPPA2 were not strengthened in the second stage. Survival studies of larger size or more extreme or specific phenotypes may support or refine these initial findings.

  1. 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.

  2. 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.

  3. Cancer Epidemiology Data Repository (CEDR)

    Cancer.gov

    In an effort to broaden access and facilitate efficient data sharing, the Epidemiology and Genomics Research Program (EGRP) has created the Cancer Epidemiology Data Repository (CEDR), a centralized, controlled-access database, where Investigators can deposit individual-level de-identified observational cancer datasets.

  4. 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

  5. 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.

  6. Dairy product intake is inversely associated with metabolic syndrome in Korean adults: Anseong and Ansan cohort of the Korean Genome and Epidemiology Study.

    PubMed

    Shin, Hyehyung; Yoon, Yeong Sook; Lee, Yoonna; Kim, Cho-il; Oh, Sang Woo

    2013-10-01

    The objective of this study was to examine the relationship between dairy product intake and the incidence of metabolic syndrome (MetS) and its components among middle-aged Koreans. We examined 7,240 adults aged 40-69 yr without MetS at baseline over a 45.5-month follow-up period. They were taken from the Anseong and Ansan cohort of the Korean Genome and Epidemiology Study. Dairy product intake including milk, yogurt, and cheese was assessed with food frequency questionnaire. At the follow-up, the incidence of MetS was 17.1%. The incidences of MetS components were as follows: low HDL cholesterol (16.2%), abdominal obesity (14.0%), hypertriglyceridemia (13.8%), hyperglycemia (13.3%), and hypertension (13.1%). Adjusting for potential confounders, dairy product consumption frequency was inversely associated with the risk of MetS and abdominal obesity. Hazard ratio (HR) (95% confidence interval) for dairy product consumption more than 7 times/week compared to never was 0.75 (0.64-0.88, P for trend < 0.001) for MetS and 0.73 (0.61-0.88, P for trend < 0.001) for abdominal obesity. HR for milk intake was 0.79 for MetS and 0.82 for abdominal obesity. The results of this study suggest that daily intake of dairy products protects against the development of MetS, particularly abdominal obesity, in middle-aged Koreans.

  7. Long-Term Colonization of the Cystic Fibrosis Lung by Burkholderia cepacia Complex Bacteria: Epidemiology, Clonal Variation, and Genome-Wide Expression Alterations

    PubMed Central

    Coutinho, Carla P.; dos Santos, Sandra C.; Madeira, Andreia; Mira, Nuno P.; Moreira, Ana S.; Sá-Correia, Isabel

    2011-01-01

    Long-term respiratory infections with Burkholderia cepacia complex (Bcc) bacteria in cystic fibrosis (CF) patients generally lead to a more rapid decline in lung function and, in some cases, to a fatal necrotizing pneumonia known as the “cepacia syndrome.” Bcc bacteria are ubiquitous in the environment and are recognized as serious opportunistic pathogens that are virtually impossible to eradicate from the CF lung, posing a serious clinical threat. The epidemiological survey of Bcc bacteria involved in respiratory infections at the major Portuguese CF Treatment Center at Santa Maria Hospital, in Lisbon, has been carried out by our research group for the past 16 years, covering over 500 clinical isolates where B. cepacia and B. cenocepacia are the predominant species, with B. stabilis, B. contaminans, B. dolosa, and B. multivorans also represented. The systematic and longitudinal study of this CF population during such an extended period of time represents a unique case–study, comprehending 41 Bcc-infected patients (29 pediatric and 12 adult) of whom around 70% have been persistently colonized between 7 months and 9 years. During chronic infection, the CF airways represent an evolving ecosystem, with multiple phenotypic variants emerging from the clonal population and becoming established in the patients’ airways as the result of genetic adaptation. Understanding the evolutionary mechanisms involved is crucial for an improved therapeutic outcome of chronic infections in CF. This review focuses on our contribution to the understanding of these adaptive mechanisms based on extensive phenotypic, genotypic, and genome-wide expression approaches of selected Bcc clonal variants obtained during long-term colonization of the CF airways. PMID:22919578

  8. Population structure and transmission dynamics of Plasmodium vivax in the Republic of Korea based on microsatellite DNA analysis.

    PubMed

    Iwagami, Moritoshi; Fukumoto, Megumi; Hwang, Seung-Young; Kim, So-Hee; Kho, Weon-Gyu; Kano, Shigeyuki

    2012-01-01

    In order to control malaria, it is important to understand the genetic structure of the parasites in each endemic area. Plasmodium vivax is widely distributed in the tropical to temperate regions of Asia and South America, but effective strategies for its elimination have yet to be designed. In South Korea, for example, indigenous vivax malaria was eliminated by the late 1970s, but re-emerged from 1993. We estimated the population structure and temporal dynamics of transmission of P. vivax in South Korea using microsatellite DNA markers. We analyzed 255 South Korean P. vivax isolates collected from 1994 to 2008, based on 10 highly polymorphic microsatellite DNA loci of the P. vivax genome. Allelic data were obtained for the 87 isolates and their microsatellite haplotypes were determined based on a combination of allelic data of the loci. In total, 40 haplotypes were observed. There were two predominant haplotypes: H16 and H25. H16 was observed in 9 isolates (10%) from 1996 to 2005, and H25 in 27 (31%) from 1995 to 2003. These results suggested that the recombination rate of P. vivax in South Korea, a temperate country, was lower than in tropical areas where identical haplotypes were rarely seen in the following year. Next, we estimated the relationships among the 40 haplotypes by eBURST analysis. Two major groups were found: one composed of 36 isolates (41%) including H25; the other of 20 isolates (23%) including H16. Despite the low recombination rate, other new haplotypes that are genetically distinct from the 2 groups have also been observed since 1997 (H27). These results suggested a continual introduction of P. vivax from other population sources, probably North Korea. Molecular epidemiology using microsatellite DNA of the P. vivax population is effective for assessing the population structure and transmission dynamics of the parasites--information that can assist in the elimination of vivax malaria in endemic areas.

  9. 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

  10. Evaluation of a Phylogenetic Marker Based on Genomic Segment B of Infectious Bursal Disease Virus: Facilitating a Feasible Incorporation of this Segment to the Molecular Epidemiology Studies for this Viral Agent

    PubMed Central

    Martínez-Pérez, Orlando; Dolz, Roser; Valle, Rosa; Perera, Carmen L.; Bertran, Kateri; Frías, Maria T.; Ganges, Llilianne; Díaz de Arce, Heidy; Majó, Natàlia; Núñez, José I.; Pérez, Lester J.

    2015-01-01

    Background Infectious bursal disease (IBD) is a highly contagious and acute viral disease, which has caused high mortality rates in birds and considerable economic losses in different parts of the world for more than two decades and it still represents a considerable threat to poultry. The current study was designed to rigorously measure the reliability of a phylogenetic marker included into segment B. This marker can facilitate molecular epidemiology studies, incorporating this segment of the viral genome, to better explain the links between emergence, spreading and maintenance of the very virulent IBD virus (vvIBDV) strains worldwide. Methodology/Principal Findings Sequences of the segment B gene from IBDV strains isolated from diverse geographic locations were obtained from the GenBank Database; Cuban sequences were obtained in the current work. A phylogenetic marker named B-marker was assessed by different phylogenetic principles such as saturation of substitution, phylogenetic noise and high consistency. This last parameter is based on the ability of B-marker to reconstruct the same topology as the complete segment B of the viral genome. From the results obtained from B-marker, demographic history for both main lineages of IBDV regarding segment B was performed by Bayesian skyline plot analysis. Phylogenetic analysis for both segments of IBDV genome was also performed, revealing the presence of a natural reassortant strain with segment A from vvIBDV strains and segment B from non-vvIBDV strains within Cuban IBDV population. Conclusions/Significance This study contributes to a better understanding of the emergence of vvIBDV strains, describing molecular epidemiology of IBDV using the state-of-the-art methodology concerning phylogenetic reconstruction. This study also revealed the presence of a novel natural reassorted strain as possible manifest of change in the genetic structure and stability of the vvIBDV strains. Therefore, it highlights the need to obtain

  11. Epidemiology: Then and Now.

    PubMed

    Kuller, Lewis H

    2016-03-01

    Twenty-five years ago, on the 75th anniversary of the Johns Hopkins Bloomberg School of Public Health, I noted that epidemiologic research was moving away from the traditional approaches used to investigate "epidemics" and their close relationship with preventive medicine. Twenty-five years later, the role of epidemiology as an important contribution to human population research, preventive medicine, and public health is under substantial pressure because of the emphasis on "big data," phenomenology, and personalized medical therapies. Epidemiology is the study of epidemics. The primary role of epidemiology is to identify the epidemics and parameters of interest of host, agent, and environment and to generate and test hypotheses in search of causal pathways. Almost all diseases have a specific distribution in relation to time, place, and person and specific "causes" with high effect sizes. Epidemiology then uses such information to develop interventions and test (through clinical trials and natural experiments) their efficacy and effectiveness. Epidemiology is dependent on new technologies to evaluate improved measurements of host (genomics), epigenetics, identification of agents (metabolomics, proteomics), new technology to evaluate both physical and social environment, and modern methods of data collection. Epidemiology does poorly in studying anything other than epidemics and collections of numerators and denominators without specific hypotheses even with improved statistical methodologies.

  12. The clinical and virological features of the first imported case causing MERS-CoV outbreak in South Korea, 2015.

    PubMed

    Lee, Ji Yeon; Kim, You-Jin; Chung, Eun Hee; Kim, Dae-Won; Jeong, Ina; Kim, Yeonjae; Yun, Mi-Ran; Kim, Sung Soon; Kim, Gayeon; Joh, Joon-Sung

    2017-07-14

    In 2015, the largest outbreak of Middle East respiratory syndrome coronavirus (MERS-CoV) infection outside the Middle East occurred in South Korea. We summarized the epidemiological, clinical, and laboratory findings of the first Korean case of MERS-CoV and analyzed whole-genome sequences of MERS-CoV derived from the patient. A 68-year-old man developed fever and myalgia 7 days after returning to Korea, following a 10-day trip to the Middle East. Before diagnosis, he visited 4 hospitals, potentially resulting in secondary transmission to 28 patients. On admission to the National Medical Center (day 9, post-onset of clinical illness), he presented with drowsiness, hypoxia, and multiple patchy infiltrations on the chest radiograph. He was intubated (day 12) because of progressive acute respiratory distress syndrome (ARDS) and INF-α2a and ribavirin treatment was commenced. The treatment course was prolonged by superimposed ventilator associated pneumonia. MERS-CoV PCR results converted to negative from day 47 and the patient was discharged (day 137), following rehabilitation therapy. The complete genome sequence obtained from a sputum sample (taken on day 11) showed the highest sequence similarity (99.59%) with the virus from an outbreak in Riyadh, Saudi Arabia, in February 2015. The first case of MERS-CoV infection had high transmissibility and was associated with a severe clinical course. The patient made a successful recovery after early treatment with antiviral agents and adequate supportive care. This first case in South Korea became a super-spreader because of improper infection control measures, rather than variations of the virus.

  13. Burden of disease in Korea during 2000-10.

    PubMed

    Lee, K S; Park, J H

    2014-06-01

    This study estimates the burden of disease in Korea during 2000-10, using disability-adjusted life years (DALYs). DALYs are the sum of years of life lost from mortality and years of life lost from disability. DALYs for 24 major diseases in 2000, 2005 and 2010 Korea were calculated based on the Global Burden of Disease Study method. As in other advanced nations, the burden of disease in Korea is characterized by an increasing importance of cancer, unipolar depression and ischemic heart disease (1681, 1508 and 562 person-years for Year 2010 in terms of DALYs per 10 0000, respectively). At the same time, unipolar depression, liver cirrhosis and mental and behavioral disorder due to alcohol use (1508, 323 and 535 person-years for 2010, respectively) became much more common in Korea than in other advanced nations. The burden of disease in Korea follows the pattern of other advanced nations in general but also registers some unique characteristics affected by the nation's distinctive epidemiological and sociocultural contexts, e.g. rapid economic growth and dramatic social transition without appropriate policy response. Korea's health and welfare policy might need to incorporate these special conditions for the effective reduction of its disease burden. © The Author 2013. Published by Oxford University Press on behalf of Faculty of Public Health. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  14. 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.

  15. Genome-Wide Association Study of White Blood Cell Count in 16,388 African Americans: the Continental Origins and Genetic Epidemiology Network (COGENT)

    PubMed Central

    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.

    2011-01-01

    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

  16. 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

  17. 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

  18. Anthropometric indices as predictors of hypertension among men and women aged 40-69 years in the Korean population: the Korean Genome and Epidemiology Study.

    PubMed

    Lee, Joung-Won; Lim, Nam-Kyoo; Baek, Tae-Hwa; Park, Sung-Hee; Park, Hyun-Young

    2015-02-13

    Obesity is one of the most significant risk factors for hypertension. However, there is controversy regarding which measure is the best predictor of hypertension risk. We compared body mass index (BMI), waist circumference (WC), waist-to-hip ratio (WHR), and waist-to-height ratio (WHtR) in subjects as predictive indicators for development of hypertension. The data were obtained from the Korean Genome and Epidemiology Study (KoGES), a large population-based prospective cohort study. A total of 4,454 subjects (2,128 men and 2,326 women) aged 40-69 years who did not have hypertension at baseline were included in this study. Incident hypertension was defined as systolic blood pressure ≥140 mmHg, diastolic blood pressure ≥90 mmHg, or anti-hypertensive medication use during the 4-year follow up. Receiver operating characteristic (ROC) analysis was used to compare discrimination abilities for anthropometric indices for hypertension. Hazard ratios were calculated by Cox proportional hazard model with adjustment for age, smoking status, alcohol consumption, diabetes and family history of hypertension by sexes. In men, the area under the ROC curve (AROC) was 0.62 for WC, WHR, and WHtR and 0.58 for BMI. In women, the AROCs for BMI, WC, WHR, and WHtR were 0.57, 0.66, 0.68, and 0.68, respectively. After adjustment for risk factors, a 1 standard deviation increase in BMI, WC, WHR, WHtR were significantly related to incident hypertension, respectively (hazard ratio: 1.39, 1.50, 1.40 and 1.49 in men, 1.31, 1.44, 1.35 and 1.48 in women). The central obesity indices WC, WHR, and WHtR were better than BMI for the prediction of hypertension in middle-aged Korean people. WHtR facilitates prediction of incident hypertension because of the single standard regardless of sex, ethnicity, and age group. Therefore, WHtR is recommended as a screening tool for the prediction of hypertension.

  19. Sequencing of SCN5A identifies rare and common variants associated with cardiac conduction: Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium.

    PubMed

    Magnani, Jared W; Brody, Jennifer A; Prins, Bram P; Arking, Dan E; Lin, Honghuang; Yin, Xiaoyan; Liu, Ching-Ti; Morrison, Alanna C; Zhang, Feng; Spector, Tim D; Alonso, Alvaro; Bis, Joshua C; Heckbert, Susan R; Lumley, Thomas; Sitlani, Colleen M; Cupples, L Adrienne; Lubitz, Steven A; Soliman, Elsayed Z; Pulit, Sara L; Newton-Cheh, Christopher; O'Donnell, Christopher J; Ellinor, Patrick T; Benjamin, Emelia J; Muzny, Donna M; Gibbs, Richard A; Santibanez, Jireh; Taylor, Herman A; Rotter, Jerome I; Lange, Leslie A; Psaty, Bruce M; Jackson, Rebecca; Rich, Stephen S; Boerwinkle, Eric; Jamshidi, Yalda; Sotoodehnia, Nona

    2014-06-01

    The cardiac sodium channel SCN5A regulates atrioventricular and ventricular conduction. Genetic variants in this gene are associated with PR and QRS intervals. We sought to characterize further the contribution of rare and common coding variation in SCN5A to cardiac conduction. In Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium Targeted Sequencing Study, we performed targeted exonic sequencing of SCN5A (n=3699, European ancestry individuals) and identified 4 common (minor allele frequency >1%) and 157 rare variants. Common and rare SCN5A coding variants were examined for association with PR and QRS intervals through meta-analysis of European ancestry participants from CHARGE, National Heart, Lung, and Blood Institute's Exome Sequencing Project (n=607), and the UK10K (n=1275) and by examining Exome Sequencing Project African ancestry participants (n=972). Rare coding SCN5A variants in aggregate were associated with PR interval in European and African ancestry participants (P=1.3×10(-3)). Three common variants were associated with PR and QRS interval duration among European ancestry participants and one among African ancestry participants. These included 2 well-known missense variants: rs1805124 (H558R) was associated with PR and QRS shortening in European ancestry participants (P=6.25×10(-4) and P=5.2×10(-3), respectively) and rs7626962 (S1102Y) was associated with PR shortening in those of African ancestry (P=2.82×10(-3)). Among European ancestry participants, 2 novel synonymous variants, rs1805126 and rs6599230, were associated with cardiac conduction. Our top signal, rs1805126 was associated with PR and QRS lengthening (P=3.35×10(-7) and P=2.69×10(-4), respectively) and rs6599230 was associated with PR shortening (P=2.67×10(-5)). By sequencing SCN5A, we identified novel common and rare coding variants associated with cardiac conduction. © 2014 American Heart Association, Inc.

  20. Pediatric liver transplantation outcomes in Korea.

    PubMed

    Kim, Jong Man; Kim, Kyung Mo; Yi, Nam-Joon; Choe, Yon Ho; Kim, Myung Soo; Suh, Kyung Suk; Kim, Soon I I; Lee, Suk-Koo; Lee, Sung-Gyu

    2013-01-01

    Pediatric liver transplantation is the standard of care for treatment of liver failure in children. The aim of this study was to identify the characteristics of pediatric liver transplantation in centers located in Korea and determine factors that influence outcomes. This retrospective study was performed using data from between 1988 and 2010 and included all recipients 18 yr old and younger who underwent pediatric liver transplantation in Korea during that period. Our data sources were hospital medical records and the outcome measure was overall patient survival. Univariate and multivariate statistical analyses were undertaken using the Cox proportional hazards model. Five hundred and thirty-four pediatric liver transplantations were performed in 502 children. Median age and average pediatric end-stage liver disease (PELD) score were 20 months and 18 point, respectively. Biliary atresia (57.7%, 308/534) was the most common cause of liver disease. Eighty-two (15.3%) were deceased donor liver transplantations and 454 (84.7%) were living donor liver transplantations. Retransplantation was performed in 32 cases (6%). Overall, 1-, 5-, and 10-yr patient survival rates were 87.8%, 82.2%, and 78.1%, respectively. In multivariate analysis, independent significant predictors of poor patient survival were chronic rejection and retransplantation. This study presents the epidemiologic data for nearly all pediatric liver transplantation in Korea and shows that the independent prognostic factors in patient survival are chronic rejection and retransplantation.

  1. Prevalence of primary immunodeficiency in Korea.

    PubMed

    Rhim, Jung Woo; Kim, Kyung Hyo; Kim, Dong Soo; Kim, Bong Seong; Kim, Jung Soo; Kim, Chang Hwi; Kim, Hwang Min; Park, Hee Ju; Pai, Ki Soo; Son, Byong Kwan; Shin, Kyung Sue; Oh, Moo Young; Woo, Young Jong; Yoo, Young; Lee, Kun Soo; Lee, Kyung Yil; Lee, Chong Guk; Lee, Joon Sung; Chung, Eun Hee; Choi, Eun Hwa; Hahn, Youn Soo; Park, Hyun Young; Kim, Joong Gon

    2012-07-01

    This study represents the first epidemiological study based on the national registry of primary immunodeficiencies (PID) in Korea. Patient data were collected from 23 major hospitals. A total of 152 patients with PID (under 19 yr of age), who were observed from 2001 to 2005, have been entered in this registry. The period prevalence of PID in Korea in 2005 is 11.25 per million children. The following frequencies were found: antibody deficiencies, 53.3% (n = 81), phagocytic disorders, 28.9% (n = 44); combined immunodeficiencies, 13.2% (n = 20); and T cell deficiencies, 4.6% (n = 7). Congenital agammaglobulinemia (n = 21) and selective IgA deficiency (n = 21) were the most frequently reported antibody deficiency. Other reported deficiencies were common variable immunodeficiencies (n = 16), X-linked agammaglobulinemia (n = 15), IgG subclass deficiency (n = 4). Phagocytic disorder was mostly chronic granulomatous disease. A small number of patients with Wiskott-Aldrich syndrome, hyper-IgE syndrome, and severe combined immunodeficiency were also registered. Overall, the most common first manifestation was pneumonia. This study provides data that permit a more accurate estimation PID patients in Korea.

  2. 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

  3. Molecular Epidemiology of Human Immunodeficiency Virus

    PubMed Central

    2017-01-01

    During the evolution of human immunodeficiency virus (HIV), transmissions between humans and primates resulted in multiple HIV lineages in humans. This evolution has been rapid, giving rise to a complex classification and allowing for worldwide spread and intermixing of subtypes, which has consequently led to dozens of circulating recombinant forms. In the Republic of Korea, 12,522 cases of HIV infection have been reported between 1985, when AIDS was first identified, and 2015. This review focuses on the evolution of HIV infection worldwide and the molecular epidemiologic characteristics of HIV in Korea. PMID:28332348

  4. Overdiagnosis: epidemiologic concepts and estimation.

    PubMed

    Bae, Jong-Myon

    2015-01-01

    Overdiagnosis of thyroid cancer was propounded regarding the rapidly increasing incidence in South Korea. Overdiagnosis is defined as 'the detection of cancers that would never have been found were it not for the screening test', and may be an extreme form of lead bias due to indolent cancers, as is inevitable when conducting a cancer screening programme. Because it is solely an epidemiological concept, it can be estimated indirectly by phenomena such as a lack of compensatory drop in post-screening periods, or discrepancies between incidence and mortality. The erstwhile trials for quantifying the overdiagnosis in screening mammography were reviewed in order to secure the data needed to establish its prevalence in South Korea.

  5. 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.

  6. 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…

  7. 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…

  8. 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…

  9. Educational Facilities in Korea.

    ERIC Educational Resources Information Center

    PEB Exchange, 1999

    1999-01-01

    Describes a Korean program to modernize school buildings and equipment to better meet current teaching needs.Examines Korea's education and administrative systems, and the Ministry of Education's involvement in schooling trends, facilities for higher education, and developments in information and technology. (GR)

  10. 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…

  11. High-quality draft genome sequence of Flavobacterium suncheonense GH29-5T (DSM 17707T) isolated from greenhouse soil in South Korea, and emended description of Flavobacterium suncheonense GH29-5T

    SciTech Connect

    Tashkandy, Nisreen; Sabban, Sari; Fakieh, Mohammad; Meier-Kolthoff, Jan P.; Huang, Sixing; Tindall, Brian J.; Rohde, Manfred; Baeshen, Mohammed N.; Baeshen, Nabih A.; Lapidus, Alla; Copeland, Alex; Pillay, Manoj; Reddy, T. B. K.; Huntemann, Marcel; Pati, Amrita; Ivanova, Natalia; Markowitz, Victor; Woyke, Tanja; Göker, Markus; Klenk, Hans-Peter; Kyrpides, Nikos C.; Hahnke, Richard L.

    2016-06-16

    Flavobacterium suncheonense is a member of the family Flavobacteriaceae in the phylum Bacteroidetes. Strain GH29-5 T (DSM 17707 T ) was isolated from greenhouse soil in Suncheon, South Korea. F. suncheonense GH29-5 T is part of the Genomic Encyclopedia of Bacteria and Archaea project. The 2,880,663 bp long draft genome consists of 54 scaffolds with 2739 protein-coding genes and 82 RNA genes. The genome of strain GH29-5 T has 117 genes encoding peptidases but a small number of genes encoding carbohydrate active enzymes (51 CAZymes). Metallo and serine peptidases were found most frequently. Among CAZymes, eight glycoside hydrolase families, nine glycosyl transferase families, two carbohydrate binding module families and four carbohydrate esterase families were identified. Suprisingly, polysaccharides utilization loci (PULs) were not found in strain GH29-5 T . Based on the coherent physiological and genomic characteristics we suggest that F. suncheonense GH29-5 T feeds rather on proteins than saccharides and lipids.

  12. 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

  13. Prevalence of vitiligo and associated comorbidities in Korea.

    PubMed

    Lee, Hemin; Lee, Mu-Hyoung; Lee, Dong Youn; Kang, Hee Young; Kim, Ki Ho; Choi, Gwang Seong; Shin, Jeonghyun; Lee, Hee Jung; Kim, Dong Hyun; Kim, Tae Heung; Lee, Ai-Young; Lee, Seung Chul; Lee, Sanghoon; Kim, Kyoung Wan; Hann, Seung-Kyung; Park, Chul Jong; Oh, Sang Ho

    2015-05-01

    Vitiligo prevalence and its associated comorbidities rate have been reported variably among different populations. We aimed to determine the prevalence of vitiligo in Korea along with the baseline rate of comorbidities and compared the risks to the general population using hospital visit information of the total population in Korea. We assessed demographic characteristics of vitiligo patients in Korean population from 2009 to 2011 in a nationwide data from Health Insurance Review Assessment Service. Patients who had at least one visit to Korea's primary, secondary, or tertiary referral hospitals with International Classification of Diseases, 10th Revision, Clinical Modification diagnosis code for vitiligo were identified. As a supplementary study, comorbidities associated with vitiligo were selected for further review to calculate relative risks compared to the general population. The annual prevalence of vitiligo determined by hospital-visiting rate in Korea was 0.12% to 0.13% over a three year period. In sync with other previous epidemiological studies, there was bimodal distribution among the age groups and no difference between genders. Also, vitiligo in Korean population was associated with various autoimmune/non-autoimmune diseases such as thyroiditis, atopic dermatitis, and psoriasis. This study was by far the most comprehensive review on prevalence of vitiligo using a data of total population in Korea. The prevalence is within a range of those reported in previous literatures, and increased risk of comorbidities such as thyroid diseases and psoriasis in vitiligo might aid clinicians in the initial work up of vitiligo patients and concurrent follow ups.

  14. East Asia: Korea.

    DTIC Science & Technology

    1988-07-18

    CHOSON Reviews Korean Army 13 ECONOMIC Samsung Group Moves Toward Merger, Expansion 34 Production of Export Goods Diversified 35 Rapid Information...events and the income from the sale of TV broadcasting privileges." However, the IOC and the Korean Olympic Committee (KOC) of Seoul have taken the...explanation into rumors that 6.5 million U.S. dollars was received as a commis- sion for Korea’s purchase of u.s. weapons during the Chon government, as

  15. South Korea Leads the Warfight

    DTIC Science & Technology

    2007-01-01

    warfighting command in a doctrinally supporting relationship to the ROK armed forces. The evolution to a Korean -led defense of the Republic of Korea is a...T he Republic of Korea –U.S. alliance is embarking on the most profound transformation affecting American forces on the peninsula since the Korean ...War. For the last 57 years, the United States has led the war- fighting command responsible for the defense of the Republic of Korea (ROK). As the ROK

  16. GSDC: A Unique Data Center in Korea for HEP research

    NASA Astrophysics Data System (ADS)

    Ahn, Sang-Un

    2017-04-01

    Global Science experimental Data hub Center (GSDC) at Korea Institute of Science and Technology Information (KISTI) is a unique data center in South Korea established for promoting the fundamental research fields by supporting them with the expertise on Information and Communication Technology (ICT) and the infrastructure for High Performance Computing (HPC), High Throughput Computing (HTC) and Networking. GSDC has supported various research fields in South Korea dealing with the large scale of data, e.g. RENO experiment for neutrino research, LIGO experiment for gravitational wave detection, Genome sequencing project for bio-medical, and HEP experiments such as CDF at FNAL, Belle at KEK, and STAR at BNL. In particular, GSDC has run a Tier-1 center for ALICE experiment using the LHC at CERN since 2013. In this talk, we present the overview on computing infrastructure that GSDC runs for the research fields and we discuss on the data center infrastructure management system deployed at GSDC.

  17. Tsunami Catalog in Korea

    NASA Astrophysics Data System (ADS)

    Jin, Sobeom; Hyun, Seung Gyu; Noh, Myunghyun

    2015-04-01

    Significant tsunamis are described in historic and instrumental earthquake sources for all regions around the Korean Peninsula. According to the low seismicity near the Peninsula, there are relatively few tsunami events in Korea. Most of the tsunami events are associated with big earthquakes at the eastern margin of the East Sea. One historical event is associated with a volcanic eruption. For that reason, the eastern coast of the Korean Peninsula is the affectable area for tsunami. One historical event at the Yellow Sea area is inferred a result from a big earthquake in China. And one plate boundary earthquake between the Philippine Plate and the Eurasian Plate affected to an island located in south of the Korean Peninsula. We confirmed the historic tsunami events by review the foreign literatures. More detailed information is presented for the instrumental earthquake source events. This work was supported by the Nuclear Safety Research Program through the Korea Radiation Safety Foundation (KORSAFe) and the Nuclear Safety and Security Commission (NSSC), Republic of Korea (Grant No. 1305001).

  18. 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.

  19. Characterization of norovirus infections in Seoul, Korea.

    PubMed

    Park, Sanghun; Jung, Jihun; Oh, Seah; Jung, Hyowon; Oh, Younghee; Cho, Seokju; Cho, Seogju; Cho, Sungja; Park, Hyongsug; Jo, Namsook; Bae, Kyungwon; Choi, Sungmin; Kim, Bogsoon; Kim, Junghun; Chae, Youngzoo; Jung, Haesook; Cheon, Doosung; Kim, Hyunsoo

    2012-10-01

    The present study has determined the detection rate of norovirus (NoV) with acute gastroenteritis (AGE) in hospitalized children and describes the molecular epidemiology of NoV circulating in Seoul, Korea. Six hundred and eighty-three (9.8%) of samples were positive for NoV. Of these, the NoV GII genogroup was the most commonly found, with a prevalence of 96.2% (683 of 710). Only 27 samples were positive for the NoV GI genogroup. Ten kinds of GI genotype (GI/1, GI/2, GI/3, GI/4, GI/5, GI/6, GI/7, GI/9, GI/12, and GI/13) and eight kinds of GII genotype (GII/2, GII/3, GII/4, GII/8, GII/14, GII/15, GII/16, and GII/17) were identified in children with AGE during the years 2008-2011.

  20. Environmental asbestos exposure sources in Korea.

    PubMed

    Kang, Dong-Mug; Kim, Jong-Eun; Kim, Ju-Young; Lee, Hyun-Hee; Hwang, Young-Sik; Kim, Young-Ki; Lee, Yong-Jin

    2016-10-01

    Because of the long asbestos-related disease latencies (10-50 years), detection, diagnosis, and epidemiologic studies require asbestos exposure history. However, environmental asbestos exposure source (EAES) data are lacking. To survey the available data for past EAES and supplement these data with interviews. We constructed an EAES database using a literature review and interviews of experts, former traders, and workers. Exposure sources by time period and type were visualized using a geographic information system (ArcGIS), web-based mapping (Google Maps), and OpenWeatherMap. The data were mounted in the GIS to show the exposure source location and trend. The majority of asbestos mines, factories, and consumption was located in Chungnam; Gyeonggi, Busan, and Gyeongnam; and Gyeonggi, Daejeon, and Busan, respectively. Shipbuilding and repair companies were mostly located in Busan and Gyeongnam. These tools might help evaluate past exposure from EAES and estimate the future asbestos burden in Korea.

  1. [Circulatory disease surveillance system in Korea].

    PubMed

    Chun, Byung-Yeol

    2007-07-01

    The purpose of establishing the circulatory disease surveillance system in Korea is to ensure that the problems of circulatory disease importance are being monitored efficiently and effectively. The goals of circulatory disease surveillance system are to monitor the epidemiological trends of circulatory disease and to evaluate the outcome of health activity for controlling circulatory diseases. Surveillance system are being updated to achieve the needs for the integration of the surveillance and information system, the establishment of data standards, the electronic exchange of data, and changes in the goals of circulatory disease surveillance system to facilitate the response of this system to manage the national health problem effectively. This article provides the target diseases and determinant indicators to be monitored, structure of circulatory disease surveillance system, and many tasks and related activities that should be applied to this system.

  2. Ionizing Radiation-induced Diseases in Korea

    PubMed Central

    Jeong, Meeseon; Moon, Kieun; Jo, Min-Heui; Kang, Seong-Kyu

    2010-01-01

    Radiation risk has become well known through epidemiological studies of clinically or occupationally exposed populations, animal experiments, and in vitro studies; however, the study of radiation related or induced disease has been limited in Korea. This study is to find the level of occupational radiation exposure for various kinds of accidents, compensated occupational diseases, related studies, and estimations on future occupational disease risks. Research data of related institutions were additionally investigated. About 67% of 62,553 radiation workers had no exposure or less than 1.2 mSv per year. The 5 reported cases on radiation accident patients in Korea occurred during nondestructive testing. According to the recent rapid increase in the number of workers exposed to radiation, a higher social recognition of cancer, and an increasing cancer mortality rate, it is expected that occupational disease compensation will rapidly increase as well. Therefore, it is important to develop scientific and objective decision methods, such as probability of causation and screening dose in the establishment of an exposure and health surveillance system. PMID:21258594

  3. Clinical Characteristics of Cholinergic Urticaria in Korea

    PubMed Central

    Kim, Jung Eun; Eun, Young Sun; Park, Young Min; Park, Hyun Jeong; Yu, Dong Su; Kang, Hoon; Cho, Sang Hyun; Park, Chul Jong; Kim, Si Yong

    2014-01-01

    Background Cholinergic urticaria is a type of physical urticaria characterized by heat-associated wheals. Several reports are available about cholinergic urticaria; however, the clinical manifestations and pathogenesis are incompletely understood. Objective The purpose of this study was to investigate the clinical characteristics of cholinergic urticaria in Korea. Methods We performed a retrospective study of 92 patients with cholinergic urticaria who were contacted by phone and whose diagnoses were confirmed by the exercise provocation test among those who had visited The Catholic University of Korea, Catholic Medical Center from January 2001 to November 2010. Results All 92 patients were male, and their average age was 27.8 years (range, 17~51 years). Most of the patients had onset of the disease in their 20s and 30s. Non-follicular wheals were located on the trunk and upper extremities of many patients, and the symptoms were aggravated by exercise. Eight patients showed general urticaria symptoms and 15 had accompanying atopic disease. Forty-three patients complained of seasonal aggravation. Most patients were treated with first and second-generation antihistamines. Conclusion Dermatologists should consider these characteristics in patients with cholinergic urticaria. Further investigation and follow-up studies are necessary to better understand the epidemiological and clinical findings of cholinergic urticaria. PMID:24882973

  4. 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

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

    PubMed

    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.

  6. 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

  7. Traditional medicine and genomics

    PubMed Central

    Joshi, Kalpana; Ghodke, Yogita; Shintre, Pooja

    2010-01-01

    ‘Omics’ developments in the form of genomics, proteomics and metabolomics have increased the impetus of traditional medicine research. Studies exploring the genomic, proteomic and metabolomic basis of human constitutional types based on Ayurveda and other systems of oriental medicine are becoming popular. Such studies remain important to developing better understanding of human variations and individual differences. Countries like India, Korea, China and Japan are investing in research on evidence-based traditional medicines and scientific validation of fundamental principles. This review provides an account of studies addressing relationships between traditional medicine and genomics. PMID:21829298

  8. Fires and smoke in Korea

    NASA Technical Reports Server (NTRS)

    2002-01-01

    The Moderate resolution Imaging Spectroradiometer (MODIS) on the Terra satellite detected several fires burning in South Korea on June 6, 2002. The smoke is blanketing both South and North Korea, and may be mingling with smoke from other fires in China. Beneath the haze, colored water at the southern tip of the Peninsula suggests sediment or phytoplankton in the coastal waters.

  9. Fires and smoke in Korea

    NASA Technical Reports Server (NTRS)

    2002-01-01

    The Moderate resolution Imaging Spectroradiometer (MODIS) on the Terra satellite detected several fires burning in South Korea on June 6, 2002. The smoke is blanketing both South and North Korea, and may be mingling with smoke from other fires in China. Beneath the haze, colored water at the southern tip of the Peninsula suggests sediment or phytoplankton in the coastal waters.

  10. 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…

  11. Molecular Epidemiology of Glanders, Pakistan

    PubMed Central

    Hornstra, Heidie; Pearson, Talima; Georgia, Shalamar; Liguori, Andrew; Dale, Julia; Price, Erin; O’Neill, Matthew; DeShazer, David; Muhammad, Ghulam; Saqib, Muhammad; Naureen, Abeera

    2009-01-01

    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. PMID:19961695

  12. 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.

  13. Whole-Genome Sequencing Applied to the Molecular Epidemiology of Shiga Toxin-Producing Escherichia coli O157:H7 in Argentina

    PubMed Central

    Fittipaldi, Nahuel; Teatero, Sarah; Athey, Taryn B. T.; Pianciola, Luis; Masana, Marcelo; Melano, Roberto G.; Rivas, Marta; Chinen, Isabel

    2016-01-01

    Shiga toxin-producing Escherichia coli strains are worldwide associated with sporadic human infections and outbreaks. In this work, we report the availability of high-quality draft whole-genome sequences for 19 O157:H7 strains isolated in Argentina. PMID:27908998

  14. Whole-Genome Sequencing Applied to the Molecular Epidemiology of Shiga Toxin-Producing Escherichia coli O157:H7 in Argentina.

    PubMed

    Carbonari, Claudia Carolina; Fittipaldi, Nahuel; Teatero, Sarah; Athey, Taryn B T; Pianciola, Luis; Masana, Marcelo; Melano, Roberto G; Rivas, Marta; Chinen, Isabel

    2016-12-01

    Shiga toxin-producing Escherichia coli strains are worldwide associated with sporadic human infections and outbreaks. In this work, we report the availability of high-quality draft whole-genome sequences for 19 O157:H7 strains isolated in Argentina. Copyright © 2016 Carbonari et al.

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

    SciTech Connect

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

    2016-03-07

    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

  16. North Korea Drought

    NASA Image and Video Library

    2015-06-29

    North Korea's state news agency reported the country is facing its worst drought in a century. Rice-growing provinces have been badly affected and more than 30% of rice paddies were parching up. A Landsat 7 image from June 29, 2002, compared with an ASTER image from June 26, 2015, shows the disparity in the rice crop. The images display vegetation in red, and bare fields in dark blue. The images cover an area of 27 x 34.5 km, and are located at 38.5 degrees north, 125.6 degrees east. http://photojournal.jpl.nasa.gov/catalog/PIA19501

  17. 15 CFR 746.4 - North Korea.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 15 Commerce and Foreign Trade 2 2011-01-01 2011-01-01 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 EAR99...

  18. 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 EAR99...

  19. 15 CFR 746.4 - North Korea.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 15 Commerce and Foreign Trade 2 2010-01-01 2010-01-01 false North Korea. 746.4 Section 746.4... CONTROLS § 746.4 North Korea. (a) Licensing Requirements. As authorized by section 6 of the Export... Democratic People's Republic of Korea (North Korea), except food and medicines classified as EAR99...

  20. 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 EAR99...

  1. 15 CFR 746.4 - North Korea.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 15 Commerce and Foreign Trade 2 2014-01-01 2014-01-01 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 EAR99...

  2. Molecular epidemiology of influenza A/H3N2 viruses circulating in Mexico from 2003 to 2012.

    PubMed

    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.

  3. Environmental epidemiology

    SciTech Connect

    Kopfler, F.C.; Craun, G.F.

    1986-01-01

    This volume is a compendium of peer-reviewed papers presented at the Symposium on Exposure Measurement and Evaluation Methods for Epidemiology, cosponsored in 1985 by the Health Effects Research Laboratory, USEPA, and the Division of Environmental Chemistry of the American Chemical Society. The book is divided into four sections: Use of Biological Monitoring to Assess Exposure, Epidemiologic Considerations for Assessing Exposure, Health and Exposure Data Bases, and Assessment of Exposure to Environmental Contaminants for Epidemiologic Studies. Both background papers and detailed reports of human studies are presented. The Biological Monitoring section contains reports of efforts to quantify adducts in blood and urine samples. In the section on Epidemiologic Considerations the feasibility of conducting epidemiologic studies of persons residing near hazardous waste sites and those exposed to arsenic in drinking water is described. The review of Data Bases includes government and industry water quality monitoring systems, the FDA Market Basket Study, major EPA air monitoring data, the National Database on Body Burden of Toxic chemicals, and the National Human Adipose Tissue Survey. Methods of assessing current exposure and estimating past exposure are detailed in the final section. Exposure to trichloroethylene in shower water, the relationship between water quality and cardiovascular disease, the contribution of environmental lead exposures to pediatric blood lead levels, and data from the TEAM study in which researchers compare indoor, outdoor, and breath analysis of air pollutant exposures are also discussed.

  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 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

  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

    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.

  6. Clinical neuropsychology in South Korea.

    PubMed

    Kim, Myung-Sun; Chey, Jeanyung

    2016-11-01

    Clinical neuropsychology in South Korea, albeit its relatively short history, has advanced dramatically. We review a brief history and current status of clinical neuropsychology in South Korea. The history, the educational pathway, the training pathway, the certification process, and careers in clinical neuropsychology in South Korea are reviewed. We have reviewed the neuropsychological services, including assessment and treatment, research on neurological and psychiatric populations, and neuropsychology education and the requirements related to education, training, and board examinations of those providing neuropsychological services in South Korea. We also describe how the Korean Society for Neuropsychology Research, the first and only meeting for neuropsychologists in the country established in 1999, has played a major role in how clinical neuropsychology is practiced and developed as a professional field in South Korea. Clinical neuropsychology in South Korea has achieved major progress over just a quarter of a century, and its future is promising in light of the increasing demand for neuropsychological services and advances in neuroscience in the country. Challenges that the community of clinical neuropsychologists are currently facing in South Korea, including formalizing neuropsychological curriculum and training programs and developing advanced credentialing procedures, are discussed.

  7. A Locally Acquired Falciparum Malaria via Nosocomial Transmission in Korea

    PubMed Central

    Kim, Jung-Yeon; Kim, Jeong-Su; Park, Mi-Hyun; Kang, Young-A; Kwon, Jun-Wook; Cho, Shin-Hyeong; Lee, Byeong-Chul; Kim, Tong-Soo

    2009-01-01

    A 57-year old man who was admitted to an emergency room of a tertiary hospital with hemoptysis developed malarial fever 19 days later and then died from severe falciparum malaria 2 days later. He had not traveled outside of Korea for over 30 years. Through intensive interviews and epidemiological surveys, we found that a foreign patient with a recent history of travel to Africa was transferred to the same hospital with severe falciparum malaria. We confirmed through molecular genotyping of the MSP-1 gene that Plasmodium falciparum genotypes of the 2 patients were identical. It is suggested that a breach of standard infection control precautions resulted in this P. falciparum transmission between 2 patients in a hospital environment. This is the first report of a nosocomial transmission of falciparum malaria in Korea. PMID:19724701

  8. 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

  9. Health inequalities policy in Korea: current status and future challenges.

    PubMed

    Khang, Young-Ho; Lee, Sang-il

    2012-05-01

    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.

  10. Epidemiology of gliomas.

    PubMed

    Ostrom, Quinn T; Gittleman, Haley; Stetson, Lindsay; Virk, Selene M; Barnholtz-Sloan, Jill S

    2015-01-01

    Gliomas are the most common type of primary intracranial tumors. Some glioma subtypes cause significant mortality and morbidity that are disproportionate to their relatively rare incidence. A very small proportion of glioma cases can be attributed to inherited genetic disorders. Many potential risk factors for glioma have been studied to date, but few provide explanation for the number of brain tumors identified. The most significant of these factors includes increased risk due to exposure to ionizing radiation, and decreased risk with history of allergy or atopic disease. The potential effect of exposure to cellular phones has been studied extensively, but the results remain inconclusive. Recent genomic analyses, using the genome-wide association study (GWAS) design, have identified several inherited risk variants that are associated with increased glioma risk. The following chapter provides an overview of the current state of research in the epidemiology of intracranial glioma.

  11. HIV-1 Transmission Networks Across South Korea.

    PubMed

    Ahn, Mi Young; Wertheim, Joel O; Kim, Woo Joo; Kim, Shin-Woo; Lee, Jin Soo; Ann, Hea Won; Jeon, Yongduk; Ahn, Jin Young; Song, Je Eun; Oh, Dong Hyun; Kim, Yong Chan; Kim, Eun Jin; Jung, In Young; Kim, Moo Hyun; Jeong, Wooyoung; Jeong, Su Jin; Ku, Nam Su; Kim, June Myung; Smith, Davey M; Choi, Jun Yong

    2017-03-27

    Molecular epidemiology can help clarify the properties and dynamics of HIV-1 transmission networks in both global and regional scales. We studied 143 HIV-1-infected individuals recruited from four medical centers of three cities in South Korea between April 2013 and May 2014. HIV-1 env V3 sequence data were generated (337-793 bp) and analyzed using a pairwise distance-based clustering approach to infer putative transmission networks. Participants whose viruses were ≤2.0% divergent according to Tamura-Nei 93 genetic distance were defined as clustering. We collected demographic, risk, and clinical data and analyzed these data in relation to clustering. Among 143 participants, we identified nine putative transmission clusters of different sizes (range 2-4 participants). The reported risk factor of participants were concordant in only one network involving two participants, that is, both individuals reported homosexual sex as their risk factor. The participants in the other eight networks did not report concordant risk factors, although they were phylogenetically linked. About half of the participants refused to report their risk factor. Overall, molecular epidemiology provides more information to understand local transmission networks and the risks associated with these networks.

  12. 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.

  13. Occupational Asthma in Korea

    PubMed Central

    Kim, Kyoo Sang

    2010-01-01

    Occupational asthma (OA) is the leading occupational respiratory disease. Cases compensated as OA by the Korea Workers' Compensation and Welfare Service (COMWEL) (218 cases), cases reported by a surveillance system (286 cases), case reports by related scientific journals and cases confirmed by the Occupational Safety and Health Research Institute (OSHRI) over 15 yr from 1992 to 2006 were analyzed. Annual mean incidence rate was 1.6 by compensation and 3.5 by surveillance system, respectively. The trend appeared to increase according to the surveillance system. Incidence was very low compared with other countries. The most frequently reported causative agent was isocyanate followed by reactive dye in dyeing factories. Other chemicals, metals and dust were also found as causative agents. OA was underreported according to compensation and surveillance system data. In conclusion, a more effective surveillance system is needed to evaluate OA causes and distribution, and to effectively prevent newly developing OA. PMID:21258586

  14. Occupational Infection in Korea

    PubMed Central

    Ahn, Yeon-Soon; Jeong, Jae Sim

    2010-01-01

    Occupational infection is a human disease caused by work-associated exposure to microbial agents through human and environmental contact. According to the literature, occupational infection was the third leading cause of occupational disease (861 cases, 8.0%), and health care, agricultural, forestry, and fishery workers were risk groups in Korea. In addition, most high-risk groups have not been protected by workers' compensation, which could lead to underestimation of the exact spectrum and magnitude of the problem, and may also result in a lack of development and implementation of occupational infection management. Through a review of national guidelines and documentations on prevention and control of occupational infection, a management strategy would promote adherence to worker safety regulations if it is explicit with regard to the agent and mode of infection in each of the high-risk groups. PMID:21258592

  15. Epidemiology of foodborne Norovirus outbreak in Incheon, Korea.

    PubMed

    Yu, Jun-Hwan; Kim, Na-Yeon; Koh, Yeon-Ja; Lee, Hun-Jae

    2010-08-01

    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.

  16. Epidemiology of burns caused by moxibustion in Korea.

    PubMed

    Yoon, Cheonjae; Cho, Young Soon; Park, Seungchoon; Chung, Sung Phil; Choi, Young Hwan

    2016-11-01

    Moxibustion, a traditional Chinese treatment that uses dried Artemisia argyi, is a common cause of burns treated in Korean hospitals. We aimed to examine the characteristics of moxibustion-induced burns. This retrospective study examined the records of 59 patients who were treated for moxibustion-induced burns (April 2014-October 2015). All patients completed a questionnaire regarding their general characteristics and moxibustion use. The patients included 16 men and 43 women (average age: 49.1 years, 68 burn sites). Superficial second-degree burns were present at 21 sites, deep second- or third-degree burns at 44 sites, and unknown burns at 3 sites. The most common sites were the lower extremities, abdomen, and upper extremities. The most common practitioners were the patients (27/59, 45.7%) and Oriental medicine practitioners (23/59, 38.9%). The most common locations were the patient's home, Oriental medicine clinic, and moxibustion clinic. The most common reason for moxibustion was pain. Only the burn site was significantly associated with burn depth, and non-abdominal sites were 9.37-fold more likely to involve deep burns (vs. abdominal sites). Korean patients routinely undergo moxibustion, and care must be taken when using moxibustion at non-abdominal sites, due to the risk of deep burns. Copyright © 2016 Elsevier Ltd and ISBI. All rights reserved.

  17. Prevalence of Vitiligo and Associated Comorbidities in Korea

    PubMed Central

    Lee, Hemin; Lee, Mu-Hyoung; Lee, Dong Youn; Kang, Hee Young; Kim, Ki Ho; Choi, Gwang Seong; Shin, Jeonghyun; Lee, Hee Jung; Kim, Dong Hyun; Kim, Tae Heung; Lee, Ai-Young; Lee, Seung Chul; Lee, Sanghoon; Kim, Kyoung Wan; Hann, Seung-Kyung

    2015-01-01

    Purpose Vitiligo prevalence and its associated comorbidities rate have been reported variably among different populations. We aimed to determine the prevalence of vitiligo in Korea along with the baseline rate of comorbidities and compared the risks to the general population using hospital visit information of the total population in Korea. Materials and Methods We assessed demographic characteristics of vitiligo patients in Korean population from 2009 to 2011 in a nationwide data from Health Insurance Review Assessment Service. Patients who had at least one visit to Korea's primary, secondary, or tertiary referral hospitals with International Classification of Diseases, 10th Revision, Clinical Modification diagnosis code for vitiligo were identified. As a supplementary study, comorbidities associated with vitiligo were selected for further review to calculate relative risks compared to the general population. Results The annual prevalence of vitiligo determined by hospital-visiting rate in Korea was 0.12% to 0.13% over a three year period. In sync with other previous epidemiological studies, there was bimodal distribution among the age groups and no difference between genders. Also, vitiligo in Korean population was associated with various autoimmune/non-autoimmune diseases such as thyroiditis, atopic dermatitis, and psoriasis. Conclusion This study was by far the most comprehensive review on prevalence of vitiligo using a data of total population in Korea. The prevalence is within a range of those reported in previous literatures, and increased risk of comorbidities such as thyroid diseases and psoriasis in vitiligo might aid clinicians in the initial work up of vitiligo patients and concurrent follow ups. PMID:25837178

  18. Baektu Mountain, China & North Korea

    NASA Image and Video Library

    2014-07-14

    This image from NASA Terra spacecraft shows Baektu Mountain, an active volcano on the border between North Korea and China. Rising to 2744 m, its summit caldera is filled with a crater lake, Heaven Lake.

  19. EPA Collaboration with South Korea

    EPA Pesticide Factsheets

    EPA, the Ministry of Environment of Korea, and partner agencies in both countries cooperate to strengthen environmental governance, improve air and water quality, and reduce exposure to toxic chemicals.

  20. South Korea and the Future.

    ERIC Educational Resources Information Center

    Shin, Se Ho

    1988-01-01

    Examines projections about the future of Korea, predicting a highly diversified society built upon industrialization and moving toward an information society. Discusses the growing middle class and its societal implications and considers the effects of the country's increasing democratization. (GEA)

  1. North Korea: Terrorism List Removal

    DTIC Science & Technology

    2010-01-06

    Chin Se-ku. Yongbyon nuclear facility can be disabled within a year. JongAng Ilbo (internet version), March 13, 2007. 30 Abductions by N. Korea not...3007. 33 Choe Sang- hun and David E. Sanger, North Korea claims U.S. will remove sanctions, International Herald Tribune, September 4, 2007, p. 5...spring of 2007 to smuggle conventional arms, including machine guns , automatic rifles, and anti-tank rocket launchers, to the Tamil Tigers in Sri

  2. 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.

  3. Trans-ethnic fine-mapping of genetic loci for body mass index in the diverse ancestral populations of the Population Architecture using Genomics and Epidemiology (PAGE) Study reveals evidence for multiple signals at established loci.

    PubMed

    Fernández-Rhodes, Lindsay; Gong, Jian; Haessler, Jeffrey; Franceschini, Nora; Graff, Mariaelisa; Nishimura, Katherine K; Wang, Yujie; Highland, Heather M; Yoneyama, Sachiko; Bush, William S; Goodloe, Robert; Ritchie, Marylyn D; Crawford, Dana; Gross, Myron; Fornage, Myriam; Buzkova, Petra; Tao, Ran; Isasi, Carmen; Avilés-Santa, Larissa; Daviglus, Martha; Mackey, Rachel H; Houston, Denise; Gu, C Charles; Ehret, Georg; Nguyen, Khanh-Dung H; Lewis, Cora E; Leppert, Mark; Irvin, Marguerite R; Lim, Unhee; Haiman, Christopher A; Le Marchand, Loic; Schumacher, Fredrick; Wilkens, Lynne; Lu, Yingchang; Bottinger, Erwin P; Loos, Ruth J L; Sheu, Wayne H-H; Guo, Xiuqing; Lee, Wen-Jane; Hai, Yang; Hung, Yi-Jen; Absher, Devin; Wu, I-Chien; Taylor, Kent D; Lee, I-Te; Liu, Yeheng; Wang, Tzung-Dau; Quertermous, Thomas; Juang, Jyh-Ming J; Rotter, Jerome I; Assimes, Themistocles; Hsiung, Chao A; Chen, Yii-Der Ida; Prentice, Ross; Kuller, Lewis H; Manson, JoAnn E; Kooperberg, Charles; Smokowski, Paul; Robinson, Whitney R; Gordon-Larsen, Penny; Li, Rongling; Hindorff, Lucia; Buyske, Steven; Matise, Tara C; Peters, Ulrike; North, Kari E

    2017-06-01

    Most body mass index (BMI) genetic loci have been identified in studies of primarily European ancestries. The effect of these loci in other racial/ethnic groups is less clear. Thus, we aimed to characterize the generalizability of 170 established BMI variants, or their proxies, to diverse US populations and trans-ethnically fine-map 36 BMI loci using a sample of >102,000 adults of African, Hispanic/Latino, Asian, European and American Indian/Alaskan Native descent from the Population Architecture using Genomics and Epidemiology Study. We performed linear regression of the natural log of BMI (18.5-70 kg/m(2)) on the additive single nucleotide polymorphisms (SNPs) at BMI loci on the MetaboChip (Illumina, Inc.), adjusting for age, sex, population stratification, study site, or relatedness. We then performed fixed-effect meta-analyses and a Bayesian trans-ethnic meta-analysis to empirically cluster by allele frequency differences. Finally, we approximated conditional and joint associations to test for the presence of secondary signals. We noted directional consistency with the previously reported risk alleles beyond what would have been expected by chance (binomial p < 0.05). Nearly, a quarter of the previously described BMI index SNPs and 29 of 36 densely-genotyped BMI loci on the MetaboChip replicated/generalized in trans-ethnic analyses. We observed multiple signals at nine loci, including the description of seven loci with novel multiple signals. This study supports the generalization of most common genetic loci to diverse ancestral populations and emphasizes the importance of dense multiethnic genomic data in refining the functional variation at genetic loci of interest and describing several loci with multiple underlying genetic variants.

  4. Association of Levels of Fasting Glucose and Insulin with Rare Variants at the Chromosome 11p11.2-MADD Locus: the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Targeted Sequencing Study

    PubMed Central

    Nikpoor, Naghmeh; Morrison, Alanna C.; Chu, Huan; Ahn, Byung Soo; Wang, Shuai; Dauriz, Marco; Barzilay, Joshua I.; Dupuis, Josée; Florez, Jose C.; Coresh, Josef; Gibbs, Richard A.; Kao, W.H. Linda; Liu, Ching-Ti; McKnight, Barbara; Muzny, Donna; Pankow, James S.; Reid, Jeffrey G.; White, Charles C.; Johnson, Andrew D.; Wong, Tien Y.; Psaty, Bruce M.; Boerwinkle, Eric; Rotter, Jerome I; Siscovick, David S.; Sladek, Robert; Meigs, James B.

    2014-01-01

    Background Common variation at the 11p11.2 locus, encompassing MADD, ACP2, NR1H3, MYBPC3 and SPI1, has been associated in genome-wide association studies with fasting glucose (FG) and insulin (FI). In the Cohorts for Heart and Aging Research in Genomic Epidemiology Targeted Sequencing Study, we sequenced five gene regions at 11p11.2 to identify rare, potentially functional variants influencing FG or FI levels. Method & Results Sequencing (mean depth 38×) across 16.1kb in 3,566 non-diabetic individuals identified 653 variants, 79.9% of which were rare (MAF <1%) and novel. We analyzed rare variants in five gene regions with FI or FG using the Sequence Kernel Association Test (SKAT). At NR1H3, 53 rare variants were jointly associated with FI (p=2.73 × 10−3); of these, seven were predicted to have regulatory function and showed association with FI (p=1.28 × 10−3). Conditioning on two previously associated variants at MADD (rs7944584, rs10838687) did not attenuate this association, suggesting that there are more than two independent signals at 11p11.2. One predicted regulatory variant, chr11:47227430 (hg18; MAF 0.00068), contributed 20.6% to the overall SKAT score at NR1H3, lies in intron 2 of NR1H3 and is a predicted binding site for FOXA1, a transcription factor associated with insulin regulation. In human HepG2 hepatoma cells, the rare chr11:47227430 A allele disrupted FOXA1 binding and reduced FOXA1-dependent transcriptional activity. Conclusion Sequencing at 11p11.2- NR1H3 identified rare variation associated with FI. One variant, chr11:47227430, appears to be functional, with the rare A allele reducing transcription factor FOXA1 binding and FOXA1-dependent transcriptional activity. PMID:24951664

  5. 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

  6. [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.

  7. 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.

  8. Draft Genome Sequences of Fusobacterium nucleatum ChDC F145, ChDC F174, ChDC F206, and ChDC F300, Isolated from Human Subgingival Plaques in the Republic of Korea

    PubMed Central

    Park, Soon-Nang; Cho, Eugene; Lim, Yun Kyong; Kim, Hwa-Sook; Kim, Dae-Soo; Jung, Jaeeun; Baek, Jeong-Hun; Jo, Eojin; Chang, Young-Hyo; Shin, Jeong Hwan; Choi, Sang-Haeng; Kang, Jihee; Choi, YongUn; Park, Hong-Seog; Kim, Hongik

    2014-01-01

    Recently, five strains were isolated from human subgingival plaques and were proposed as a novel subspecies of Fusobacterium nucleatum. Here, we report the draft genome sequences of the strains, except one for which the draft sequence was already introduced. PMID:24459284

  9. Sequences and gene organization of the mitochondrial genomes of the liver flukes Opisthorchis viverrini and Clonorchis sinensis (Trematoda).

    PubMed

    Cai, X Q; Liu, G H; Song, H Q; Wu, C Y; Zou, F C; Yan, H K; Yuan, Z G; Lin, R Q; Zhu, X Q

    2012-01-01

    Opisthorchis viverrini and Clonorchis sinensis are important trematodes infecting humans and animals, belonging to the family Opisthorchiidae. In the present study, we sequenced the nearly complete mitochondrial (mt) DNA (mtDNA) sequences of O. viverrini from Laos, obtained the complete mtDNA sequences of C. sinensis from China and Korea, and revealed their gene annotations and genome organizations. The mtDNA sequences of O. viverrini, C. sinensis (China isolate), C. sinensis (Korea isolate) were 13,510, 13,879, and 13,877 bp in size, respectively. Each of the three mt genomes comprises 36 genes, consisting of 12 genes coding for proteins, two genes for rRNA, and 20 genes (O. viverrini) or 22 genes (C. sinensis) for tRNA. The gene content and arrangement are identical to that of Fasciola hepatica, and Paragonimus westermani, but distinct from Schistosoma spp. All genes are transcribed in the same direction and have a nucleotide composition high in T. The contents of A + T of the mt genomes were 59.39% for O. viverrini, 60.03% for C. sinensis (China isolate), and 59.99% for C. sinensis (Korea isolate). Phylogenetic analyses using concatenated amino acid sequences of the 12 protein-coding genes, with three different computational algorithms [maximum parsimony, maximum likelihood, and Bayesian analysis], all revealed distinct groups with high statistical support, indicating that O. viverrini and C. sinensis represent sister taxa. These data provide additional novel mtDNA markers for studying the molecular epidemiology and population genetics of the two liver flukes and should have implications for the molecular diagnosis, prevention, and control of opisthorchiasis and clonorchiasis in humans and animals.

  10. 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.

  11. An open source infrastructure for managing knowledge and finding potential collaborators in a domain-specific subset of PubMed, with an example from human genome epidemiology.

    PubMed

    Yu, Wei; Yesupriya, Ajay; Wulf, Anja; Qu, Junfeng; Khoury, Muin J; Gwinn, Marta

    2007-11-09

    Identifying relevant research in an ever-growing body of published literature is becoming increasingly difficult. Establishing domain-specific knowledge bases may be a more effective and efficient way to manage and query information within specific biomedical fields. Adopting controlled vocabulary is a critical step toward data integration and interoperability in any information system. We present an open source infrastructure that provides a powerful capacity for managing and mining data within a domain-specific knowledge base. As a practical application of our infrastructure, we presented two applications - Literature Finder and Investigator Browser - as well as a tool set for automating the data curating process for the human genome published literature database. The design of this infrastructure makes the system potentially extensible to other data sources. Information retrieval and usability tests demonstrated that the system had high rates of recall and precision, 90% and 93% respectively. The system was easy to learn, easy to use, reasonably speedy and effective. The open source system infrastructure presented in this paper provides a novel approach to managing and querying information and knowledge from domain-specific PubMed data. Using the controlled vocabulary UMLS enhanced data integration and interoperability and the extensibility of the system. In addition, by using MVC-based design and Java as a platform-independent programming language, this system provides a potential infrastructure for any domain-specific knowledge base in the biomedical field.

  12. Genomics and Health Impact Update

    MedlinePlus

    ... Publications Birth Defects/ Child Health Cancer Cardiovascular Diseases Chronic Disease Ethics, Policy and Law Genomics in Practice Newborn Screening Pharmacogenomics Reproductive Health Tools/ Databases AMD Clips News Concepts/ Comments Pathogenicity/ Antimicrobial Resistance Epidemiology/ ...

  13. Serological prevalence, genetic identification, and characterization of the first strains of avian hepatitis E virus from chickens in Korea.

    PubMed

    Kwon, Hyuk Moo; Sung, Haan Woo; Meng, Xiang-Jin

    2012-10-01

    Avian hepatitis E virus (avian HEV) is associated with hepatitis-splenomegaly (HS) syndrome or big liver and spleen disease in chickens. At least three genotypes of avian HEV have been identified from chickens worldwide. A total of 297 serum samples collected from chickens in 35 flocks in Korea were tested for avian HEV antibody with an enzyme-linked immunosorbent assay. The results showed that approximately 57 % of chicken flocks and 28 % of chickens from Korea were positive for antibodies to avian HEV. Thirteen pooled fecal samples from chickens were tested for avian HEV RNA by RT-PCR, and three fecal samples were positive. The partial helicase and capsid genes of the Korean avian HEV isolates were determined, and sequence analyses revealed that the Korean avian HEV isolates were clustered together and closely related to the genotype 1 avian HEV from Australia. The complete genomic sequence of a Korean avian HEV strain HH-F9 from a broiler breeder was determined, and shown to be 6,653 nt in length, excluding the poly (A) tail, which is 1 nt shorter than the prototype avian HEV from chicken with HS syndrome in the United States. Compared to the full-length sequences of other 5 known avian HEV strains worldwide, the Korean avian HEV shared approximately 83-97 % nucleotide sequence identity. The finding that Korean avian HEV belongs to genotype 1 avian HEV which was previously identified only from chickens in Australia has significant implication in understanding the global epidemiology of avian HEV.

  14. 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

  15. 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

  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 Korea...

  17. Sequence Variation in TMEM18 in Association with Body Mass Index: The Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Targeted Sequencing Study

    PubMed Central

    Liu, Ching-Ti; Young, Kristin L.; Brody, Jennifer; Olden, Matthias; Wojczynski, Mary K.; Heard-Costa, Nancy; Li, Guo; Morrison, Alanna C.; Muzny, Donna; Gibbs, Richard A.; Reid, Jeffrey G.; Shao, Yaming; Zhou, Yanhua; Boerwinkle, Eric; Heiss, Geraldo; Wagenknecht, Lynne; McKnight, Barbara; Borecki, Ingrid B.; Fox, Caroline S.; North, Kari E.; Cupples, L. Adrienne

    2014-01-01

    Background Genome-wide association studies (GWAS) for body mass index (BMI) previously identified a locus near TMEM18. We conducted targeted sequencing of this region to investigate the role of common, low frequency, and rare variation influencing BMI. Methods and Results We sequenced TMEM18 and regions downstream of TMEM18 on chromosome 2 in 3976 individuals of European ancestry from three community-based cohorts (Atherosclerosis Risk in Communities, Cardiovascular Health Study and Framingham Heart Study), including 200 adults selected for high BMI. We examined the association between BMI and variants identified in the region from nucleotide position 586,432 to 677,539 (hg18). Rare variants (MAF <1%) were analyzed using a burden test and the Sequence Kernel of Association Test (SKAT). Results from the three cohort studies were meta-analyzed. We estimate that mean BMI is 0.43 kg/m2 higher for each copy of the G allele of SNP rs7596758 (MAF=29%, p=3.46 × 10−4) using a Bonferroni threshold of p <4.6 × 10−4). Analyses conditional on previous GWAS SNPs associated with BMI in the region led to attenuation of this signal and uncovered another independent (r2<0.2), statistically significant association, rs186019316 (p=2.11 × 10−4). Both rs186019316 and rs7596758 or proxies are located in transcription factor binding regions. No significant association with rare variants was found in either the exons of TMEM18 or the 3’ GWAS region. Conclusions Targeted sequencing around TMEM18 identified two novel BMI variants with possible regulatory function. PMID:24951660

  18. 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.

  19. 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

  20. Distribution of lichen flora on South Korea.

    PubMed

    Hur, Jae-Seoun; Harada, Hiroshi; Oh, Soon-Ok; Lim, Kwang-Mi; Kang, Eui-Sung; Lee, Seung Mi; Kahng, Hyung-Yeel; Kim, Hyun-Woo; Jung, Jae-Sung; Koh, Young Jin

    2004-06-01

    After an overview on the temporary situation of the lichenology in South Korea, localities of 95 macrolichen taxa are reported for South Korea. In this revised lichen flora of South Korea, 16 species are apparently new to the territory. Voucher specimens have been deposited in the Korean Lichen Research Institute (KoLRI) at Sunchon National University in Korea, and duplicates have also been donated to the National History Museum and Institute, in Chiba, (CBM) Japan.

  1. 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…

  2. 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…

  3. 75 FR 67912 - North Korea Sanctions Regulations

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-11-04

    ... 31 CFR Part 510 North Korea Sanctions Regulations AGENCY: Office of Foreign Assets Control, Treasury...'') is issuing regulations with respect to North Korea to implement Executive Order 13466 of June 26... issuing the North Korea Sanctions Regulations, 31 CFR part 510 (the ``Regulations''), to implement E.O...

  4. 76 FR 35740 - North Korea Sanctions Regulations

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-06-20

    ... Part 510 North Korea Sanctions Regulations AGENCY: Office of Foreign Assets Control, Treasury. ACTION... amending the North Korea Sanctions Regulations to implement Executive Order 13570 of April 18, 2011. OFAC..., the Department of the Treasury's Office of Foreign Assets Control published the North Korea Sanctions...

  5. Genome-wide linkage and positional candidate gene study of blood pressure response to dietary potassium intervention: the genetic epidemiology network of salt sensitivity study.

    PubMed

    Kelly, Tanika N; Hixson, James E; Rao, Dabeeru C; Mei, Hao; Rice, Treva K; Jaquish, Cashell E; Shimmin, Lawrence C; Schwander, Karen; Chen, Chung-Shuian; Liu, Depei; Chen, Jichun; Bormans, Concetta; Shukla, Pramila; Farhana, Naveed; Stuart, Colin; Whelton, Paul K; He, Jiang; Gu, Dongfeng

    2010-12-01

    Genetic determinants of blood pressure (BP) response to potassium, or potassium sensitivity, are largely unknown. We conducted a genome-wide linkage scan and positional candidate gene analysis to identify genetic determinants of potassium sensitivity. A total of 1906 Han Chinese participants took part in a 7-day high-sodium diet followed by a 7-day high-sodium plus potassium dietary intervention. BP measurements were obtained at baseline and after each intervention using a random-zero sphygmomanometer. Significant linkage signals (logarithm of odds [LOD] score, >3) for BP responses to potassium were detected at chromosomal regions 3q24-q26.1, 3q28, and 11q22.3-q24.3. Maximum multipoint LOD scores of 3.09 at 3q25.2 and 3.41 at 11q23.3 were observed for absolute diastolic BP (DBP) and mean arterial pressure (MAP) responses, respectively. Linkage peaks of 3.56 at 3q25.1 and 3.01 at 11q23.3 for percent DBP response and 3.22 at 3q25.2, 3.01 at 3q28, and 4.48 at 11q23.3 for percent MAP response also were identified. Angiotensin II receptor, type 1 (AGTR1), single-nucleotide polymorphism rs16860760 in the 3q24-q26.1 region was significantly associated with absolute and percent systolic BP responses to potassium (P=0.0008 and P=0.0006, respectively). Absolute (95% CI) systolic BP responses for genotypes C/C, C/T, and T/T were -3.71 (-4.02 to -3.40), -2.62 (-3.38 to -1.85), and 1.03 (-3.73 to 5.79) mm Hg, respectively, and percent responses (95% CI) were -3.07 (-3.33 to -2.80), -2.07 (-2.74 to -1.41), and 0.90 (-3.20 to 4.99), respectively. Similar trends were observed for DBP and MAP responses. Genetic regions on chromosomes 3 and 11 may harbor important susceptibility loci for potassium sensitivity. Furthermore, the AGTR1 gene was a significant predictor of BP responses to potassium intake.

  6. 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.

  7. 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.

  8. Impact of paraquat regulation on suicide in South Korea.

    PubMed

    Cha, Eun Shil; Chang, Shu-Sen; Gunnell, David; Eddleston, Michael; Khang, Young-Ho; Lee, Won Jin

    2016-04-01

    Ingestion of pesticides (mainly paraquat) accounted for one-fifth of suicides in South Korea in 2006-10. We investigated the effect on suicide mortality of regulatory action, culminating in a ban on paraquat in South Korea in 2011-12. We calculated age-standardized method-specific suicide mortality rates among people aged ≥15 in South Korea (1983-2013) using registered death data. Negative binomial regression was used to estimate changes in the rate and number of pesticide suicides in 2013, compared with those expected based on previous trends (2003-11). Pesticide suicide mortality halved from 5.26 to 2.67 per 100 000 population between 2011 and 2013. Compared with the number expected based on previous trends, the regulations were followed by an estimated 847 [95% confidence interval (CI) -1180 to -533] fewer pesticide suicides, a 37% reduction in rates (rate ratio = 0.63, 95% CI 0.55 to 0.73) in 2013. The decline in pesticide suicides after the regulations was seen in all age/sex/geographical groups. The absolute reduction in the number of suicides was greatest among men, the elderly and in rural areas. The reduction in pesticide suicides contributed to 56% of the decline in overall suicides that occurred between 2011 and 2013. There was no impact of the regulations on crop yield. The regulation of paraquat in South Korea in 2011-12 was associated with a reduction in pesticide suicide. Further legislative interventions to prevent the easy availability of highly lethal suicide methods are recommended for reducing the number of suicides worldwide. © The Author 2015; all rights reserved. Published by Oxford University Press on behalf of the International Epidemiological Association.

  9. Asbestos-related occupational cancers compensated under the Industrial Accident Compensation Insurance in Korea.

    PubMed

    Ahn, Yeon-Soon; Kang, Seong-Kyu

    2009-04-01

    Compensation for asbestos-related cancers occurring in occupationally-exposed workers is a global issue; this is also an issue in Korea. To provide basic information regarding compensation for workers exposed to asbestos, 60 cases of asbestos-related occupational lung cancer and mesothelioma that were compensated during 15 yr; from 1993 (the year the first case was compensated) to 2007 by the Korea Labor Welfare Corporation (KLWC) are described. The characteristics of the cases were analyzed using the KLWC electronic data and the epidemiologic investigation data conducted by the Occupational Safety and Health Research Institute (OSHRI) of the Korea Occupational Safety and Health Agency (KOSHA). The KLWC approved compensation for 41 cases of lung cancer and 19 cases of mesothelioma. Males accounted for 91.7% (55 cases) of the approved cases. The most common age group was 50-59 yr (45.0%). The mean duration of asbestos exposure for lung cancer and mesothelioma cases was 19.2 and 16.0 yr, respectively. The mean latency period for lung cancer and mesothelioma cases was 22.1 and 22.6 yr, respectively. The major industries associated with mesothelioma cases were shipbuilding and maintenance (4 cases) and manufacture of asbestos textiles (3 cases). The major industries associated with lung cancer cases were shipbuilding and maintenance (7 cases), construction (6 cases), and manufacture of basic metals (4 cases). The statistics pertaining to asbestos-related occupational cancers in Korea differ from other developed countries in that more cases of mesothelioma were compensated than lung cancer cases. Also, the mean latency period for disease onset was shorter than reported by existing epidemiologic studies; this discrepancy may be related to the short history of occupational asbestos use in Korea. Considering the current Korean use of asbestos, the number of compensated cases in Korea is expected to increase in the future but not as much as developed countries.

  10. 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

  11. Dairy consumption is associated with a lower incidence of the metabolic syndrome in middle-aged and older Korean adults: the Korean Genome and Epidemiology Study (KoGES).

    PubMed

    Kim, Dasom; Kim, Jihye

    2017-01-01

    This cohort study examined the association between total and individual dairy products and the risk of developing the metabolic syndrome (MetS) and its components in Korean adults from the Korean Genome and Epidemiology Study. We prospectively analysed 5510 participants aged 40-69 years without the MetS at baseline during a 10-year follow-up period. Dairy consumption was assessed with a semi-quantitative FFQ at baseline and after 4 years. The MetS was defined according to the criteria by the National Cholesterol Education Program Adult Treatment Panel III. The Cox's proportional hazard model was used to examine the association between consumption of total dairy products, milk and yogurt in servings per week and the risk of incident MetS or individual components. A total of 2103 subjects developed the MetS (38·2 %) during an average follow-up of 67·4 months (range 17-104 months). Frequent dairy consumption (>7 servings of total dairy and milk/week, ≥4 servings of yogurt/week) was associated with a reduced risk of incident MetS and its components. In the multivariable adjusted model, hazard ratios for the MetS were 0·51 (95 % CI 0·43, 0·61) for total dairy products, 0·50 (95 % CI 0·38, 0·66) for milk and 0·67 (95 % CI 0·57, 0·78) for yogurt in frequent consumers compared with non-consumers. An inverse association between milk/yogurt and low HDL-cholesterol was shown only in women. In conclusion, high consumption of individual dairy products including milk and yogurt as well as total dairy were associated with a reduced risk of incident MetS and individual components in Korean adults.

  12. 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. Copyright © 2010 Elsevier Ltd. All rights reserved.

  13. Genome-Wide Linkage Screen for Systolic Blood Pressure in the Veterans Administration Genetic Epidemiology Study (VAGES) of Mexican-Americans and Confirmation of a Major Susceptibility Locus on Chromosome 6q14.1

    PubMed Central

    Puppala, Sobha; Coletta, Dawn K.; Schneider, Jennifer; Hu, Shirley L.; Farook, Vidya S.; Dyer, Thomas D.; Arya, Rector; Blangero, John; Duggirala, Ravindranath; DeFronzo, Ralph A.; Jenkinson, Christopher P.

    2011-01-01

    Objective Hypertension or high blood pressure is a strong correlate of diseases such as obesity and type 2 diabetes. We conducted a genome-wide linkage screen to identify susceptibility genes influencing systolic blood pressure (SBP) and diastolic blood pressure (DBP) in Mexican-Americans from the Veterans Administration Genetic Epidemiology Study (VAGES). Methods Using data from 1,089 individuals distributed across 266 families, we performed a multipoint linkage analysis to localize susceptibility loci for SBP and DBP by applying two models. In model 1, we added a sensible constant to the observed BP values in treated subjects [Tobin et al.; Stat Med 2005;24:2911–2935] to account for antihypertensive use (i.e. 15 and 10 mm Hg to SBP and DBP values, respectively). In model 2, we fixed values of 140 mm Hg for SBP and 90 mm Hg for DBP, if the treated values were less than the standard referenced treatment thresholds of 140/90 mm Hg for hypertensive status. However, if the observed treated BP values were found to be above these standard treatment thresholds, the actual observed treated BP values were retained in order not to reduce them by substitution of the treatment threshold values. Results The multipoint linkage analysis revealed strong linkage signals for SBP compared with DBP. The strongest evidence for linkage of SBP (model 1, LOD = 5.0; model 2, LOD = 3.6) was found on chromosome 6q14.1 near the marker D6S1031 (89 cM) in both models. In addition, some evidence for SBP linkage occurred on chromosomes 1q, 4p, and 16p. Most importantly, our major SBP linkage finding on chromosome 6q near marker D6S1031 was independently confirmed in a Caucasian population (LOD = 3.3). In summary, our study found evidence for a major locus on chromosome 6q influencing SBP levels in Mexican-Americans. PMID:21293138

  14. Monitoring Antifungal Resistance in a Global Collection of Invasive Yeasts and Moulds: Application of CLSI Epidemiological Cutoff Values and Whole Genome Sequencing Analysis for Detection of Azole Resistance in Candida albicans.

    PubMed

    Castanheira, Mariana; Deshpande, Lalitagauri M; Davis, Andrew P; Rhomberg, Paul R; Pfaller, Michael A

    2017-08-07

    The activity of 7 antifungal agents was evaluated against 3,557 invasive yeasts and moulds collected in 29 countries worldwide during 2014-2015. Epidemiological cutoff values (ECVs) published in the CLSI M59 document were applied for species with no clinical breakpoints. Echinocandin susceptibility rates were 95.9% to 100.0% for the 5 most common Candida species except anidulafungin and C. parapsilosis (88.7% susceptible/100.0% wild-type). Fluconazole resistance ranged from 8.0% for C. glabrata to 0.4% for C. albicans Seven Candida species displayed 100.0% wild-type amphotericin B and C. dubliniensis and C. lusitaniae exhibited wild-type echinocandin MIC results. The highest fluconazole, voriconazole, and posaconazole MIC values for Cryptococcus neoformansvar. grubii were 8 μg/mL, 0.12 μg/mL, and 0.25 μg/mL, respectively. A. fumigatus were 100.0% wild-type for caspofungin and amphotericin B, but 3 (0.8%) of these isolates were non- wild-type to itraconazole (2 isolates) or voriconazole (1 isolate). Mutations on FKS hotspots (HS) were detected among 13/20 Candida isolates (16/20 were C. glabrata) displaying echinocandin MIC>ECV. Most isolates carrying FKS HS mutations were resistant to 2 or more echinocandins. Five fluconazole-nonsusceptible C. albicans were submitted to whole genome sequencing analysis. Gain of function, Erg11 heterozygous, and Erg3 homozygous mutations were observed in 1 isolate each. One isolate displayed MDR1 promoter allele alterations associated with azole resistance. Elevated expression of MDR1 or CDR2 was observed among 3 and 1 isolates, respectively. Echinocandin and azole resistance is still uncommon among contemporary fungal isolates; however, resistance mechanisms to antifungals were observed among Candida spp. showing that resistance can emerge and monitoring is warranted. Copyright © 2017 American Society for Microbiology.

  15. Dynamic Circulation and Genetic Exchange of a Shrew-borne Hantavirus, Imjin virus, in the Republic of Korea

    PubMed Central

    Lee, Seung-Ho; Kim, Won-Keun; No, Jin Sun; Kim, Jeong-Ah; Kim, Jin Il; Gu, Se Hun; Kim, Heung-Chul; Klein, Terry A.; Park, Man-Seong; Song, Jin-Won

    2017-01-01

    Hantaviruses (family Bunyaviridae) are enveloped negative-sense tripartite RNA viruses. The natural hosts of hantaviruses include rodents, shrews, moles, and bats. Imjin virus (MJNV) is a shrew-borne hantavirus identified from the Ussuri white-toothed shrews (Crocidura lasiura) in the Republic of Korea (ROK) and China. We have isolated MJNV and determined its prevalence and molecular diversity in Gyeonggi province, ROK. However, the distribution and phylogeography of MJNV in other regions of ROK remain unknown. A total of 96 C. lasiura were captured from Gangwon and Gyeonggi provinces, ROK, during 2011–2014. Among them, four (4.2%) shrews were positive for anti-MJNV IgG and MJNV RNA was detected from nine (9.4%), respectively. Based on the prevalence of MJNV RNA, the preponderance of infected shrews was male and adult, consistent with the gender- and weight-specific prevalence of hantaviruses in other species. We monitored the viral load of MJNV RNA in various tissues of shrews, which would reflect the dynamic infectious status and circulation of MJNV in nature. Our phylogeographic and genomic characterization of MJNV suggested natural occurrences of recombination and reassortment in the virus population. Thus, these findings provide significant insights into the epidemiology, phylogeographic diversity, and dynamic circulation and evolution of shrew-borne hantaviruses. PMID:28295052

  16. Dynamic Circulation and Genetic Exchange of a Shrew-borne Hantavirus, Imjin virus, in the Republic of Korea.

    PubMed

    Lee, Seung-Ho; Kim, Won-Keun; No, Jin Sun; Kim, Jeong-Ah; Kim, Jin Il; Gu, Se Hun; Kim, Heung-Chul; Klein, Terry A; Park, Man-Seong; Song, Jin-Won

    2017-03-15

    Hantaviruses (family Bunyaviridae) are enveloped negative-sense tripartite RNA viruses. The natural hosts of hantaviruses include rodents, shrews, moles, and bats. Imjin virus (MJNV) is a shrew-borne hantavirus identified from the Ussuri white-toothed shrews (Crocidura lasiura) in the Republic of Korea (ROK) and China. We have isolated MJNV and determined its prevalence and molecular diversity in Gyeonggi province, ROK. However, the distribution and phylogeography of MJNV in other regions of ROK remain unknown. A total of 96 C. lasiura were captured from Gangwon and Gyeonggi provinces, ROK, during 2011-2014. Among them, four (4.2%) shrews were positive for anti-MJNV IgG and MJNV RNA was detected from nine (9.4%), respectively. Based on the prevalence of MJNV RNA, the preponderance of infected shrews was male and adult, consistent with the gender- and weight-specific prevalence of hantaviruses in other species. We monitored the viral load of MJNV RNA in various tissues of shrews, which would reflect the dynamic infectious status and circulation of MJNV in nature. Our phylogeographic and genomic characterization of MJNV suggested natural occurrences of recombination and reassortment in the virus population. Thus, these findings provide significant insights into the epidemiology, phylogeographic diversity, and dynamic circulation and evolution of shrew-borne hantaviruses.

  17. 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…

  18. 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…

  19. 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…

  20. North Korea: Terrorism List Removal

    DTIC Science & Technology

    2007-04-06

    15 Niksch, Larry A., North Korea and Terrorism: The Yokita Megumi Factor. The Korean Journal of Defense Analysis. Spring 2002. pp. 14-16. 16 For...remains were not those of Megumi Yokota or Kaoru Matsuki, as Pyongyang had claimed, and the issue remained contentious at year’s end. Four Japanese

  1. 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…

  2. Foreign Assistance to North Korea

    DTIC Science & Technology

    2005-05-26

    Representative for the DPRK. 41 Smith, Overcoming Humanitarian Dilemmas, p.13 Source: World Food Program, Map Resources. Adapted by CRS. (K. Yancey 3/18/04...2003 e-mail correspondence with Rick Corsino, former WFP Country Director for North Korea. 44 May 2005 e-mail correspondence with Richard Ragan, WFP

  3. 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.

  4. Population-attributable causes of cancer in Korea: obesity and physical inactivity.

    PubMed

    Park, Sohee; Kim, Yeonju; Shin, Hai-Rim; Lee, Boram; Shin, Aesun; Jung, Kyu-Won; Jee, Sun Ha; Kim, Dong Hyun; Yun, Young Ho; Park, Sue Kyung; Boniol, Mathieu; Boffetta, Paolo

    2014-01-01

    Changes in lifestyle including obesity epidemic and reduced physical activity influenced greatly to increase the cancer burden in Korea. The purpose of the current study was to perform a systematic assessment of cancers attributable to obesity and physical inactivity in Korea. Gender- and cancer site-specific population-attributable fractions (PAF) were estimated using the prevalence of overweight and obesity in 1992-1995 from a large-scale prospective cohort study, the prevalence of low physical activity in 1989 from a Korean National Health Examination Survey, and pooled relative risk estimates from Korean epidemiological studies. The overall PAF was then estimated using 2009 national cancer incidence data from the Korea Central Cancer Registry. Excess body weight was responsible for 1,444 (1.5%) and 2,004 (2.2%) cancer cases among men and women, respectively, in 2009 in Korea. Among men, 6.8% of colorectal, 2.9% of pancreatic, and 16.0% of kidney cancer was attributable to excess body weight. In women, 6.6% of colorectal, 3.9% of pancreatic, 18.7% of kidney, 8.2% of postmenopausal breast, and 32.7% of endometrial cancer was attributable to excess body weight. Low leisure-time physical activity accounted for 8.8% of breast cancer, whereas the PAF for overall cancer was low (0.1% in men, 1.4% in women). Projections suggest that cancers attributable to obesity will increase by 40% in men and 16% in women by 2020. With a significantly increasing overweight and physically inactive population, and increasing incidence of breast and colorectal cancers, Korea faces a large cancer burden