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Molecular-epidemiology

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https://www.readbyqxmd.com/read/28722566/molecular-epidemiology-of-staphylococcus-aureus-skin-and-soft-tissue-infections-in-the-lao-people-s-democratic-republic
#1
Alicia D Yeap, Kate Woods, David A B Dance, Bruno Pichon, Sayaphet Rattanavong, Viengmon Davong, Rattanaphone Phetsouvanh, Paul N Newton, Nandini Shetty, Angela M Kearns
This is the first report of the molecular epidemiology of Staphylococcus aureus from skin and soft tissue infections (SSTI) in Laos. We selected a random sample of 96 S. aureus SSTI isolates received by the Microbiology Laboratory, Mahosot Hospital, Vientiane, between July 2012 and June 2014, including representation from seven referral hospitals. Isolates underwent susceptibility testing by Clinical and Laboratory Standards Institute methods, spa typing and DNA microarray analysis, with whole genome sequencing for rare lineages...
May 30, 2017: American Journal of Tropical Medicine and Hygiene
https://www.readbyqxmd.com/read/28721851/development-and-evaluation-of-a-multiple-locus-variable-number-tandem-repeats-analysis-assay-for-subtyping-salmonella-typhi-strains-from-sub-saharan-africa
#2
Nomsa P Tau, Anthony M Smith, John R Wain, Andrew Tarupiwa, Kalpy J Coulibaly, Karen H Keddy, Germs-Sa
PURPOSE: Molecular epidemiological investigations of the highly clonal Salmonella enterica subspecies enterica serovar Typhi (S. Typhi) are important in outbreak detection and in tracking disease transmission. In this study, we developed and evaluated a multiple-locus variable-number tandem-repeats (VNTR) analysis (MLVA) assay for characterization of S. Typhi isolates from sub-Saharan Africa. METHODOLOGY: Twelve previously reported VNTR loci were evaluated and an MLVA assay consisting of five polymorphic loci was adopted...
July 18, 2017: Journal of Medical Microbiology
https://www.readbyqxmd.com/read/28719312/molecular-epidemiology-of-malaria-in-cameroon-and-c%C3%A3-te-d-ivoire-xxxi-kelch-13-propeller-sequences-in-plasmodium-falciparum-isolates-before-and-after-implementation-of-artemisinin-based-combination-therapy
#3
Joseph Allico Djaman, Dagnogo Olefongo, Aristide Berenger Ako, Jocelyne Roman, Vincent Foumane Ngane, Leonardo K Basco, Rachida Tahar
Artemisinin-resistant malaria has not been reported from Africa, but resistance can possibly spread from Asia or arise independently in Africa. The emergence of artemisinin resistance in Africa can be monitored by molecular assay of Kelch 13 (K13) propeller sequences. A total of 251 archived DNA samples of Plasmodium falciparum isolates collected in 2002, 2003, and 2006 in Yaounde, Cameroon, and 47 samples collected in 2006 and 2013 in Abidjan, Côte d'Ivoire, were analyzed for K13-propeller sequence polymorphism...
July 2017: American Journal of Tropical Medicine and Hygiene
https://www.readbyqxmd.com/read/28719296/analysis-of-dengue-serotype-4-in-sri-lanka-during-the-2012-2013-dengue-epidemic
#4
Anna Uehara, Hasitha Aravinda Tissera, Champica K Bodinayake, Ananda Amarasinghe, Ajith Nagahawatte, L Gayani Tillekeratne, Jie Cui, Megan E Reller, Paba Palihawadana, Sunethra Gunasena, Aruna Dharshan Desilva, Annelies Wilder-Smith, Duane J Gubler, Christopher W Woods, October M Sessions
The four serotypes of dengue virus (DENV-1, -2, -3, and -4) have had a rapidly expanding geographic range and are now endemic in over 100 tropical and subtropical countries. Sri Lanka has experienced periodic dengue outbreaks since the 1960s, but since 1989 epidemics have become progressively larger and associated with more severe disease. The dominant virus in the 2012 epidemic was DENV-1, but DENV-4 infections were also commonly observed. DENV-4 transmission was first documented in Sri Lanka when it was isolated from a traveler in 1978, but has been comparatively uncommon since dengue surveillance began in the early 1980s...
July 2017: American Journal of Tropical Medicine and Hygiene
https://www.readbyqxmd.com/read/28714491/molecular-epidemiology-and-antigenic-characterization-of-seasonal-influenza-viruses-circulating-in-nepal
#5
B P Upadhyay, P Ghimire, M Tashiro, M R Banjara
BACKGROUND: Influenza is one of the public health burdens in Nepal and its epidemiology is not clearly understood. The objective of this study was to explore the molecular epidemiology and the antigenic characteristics of the circulating influenza viruses in Nepal. METHODS: A total of 1495 throat swab specimens were collected from January to December, 2014. Real time PCR assay was used for identification of influenza virus types and subtypes. Ten percent of the positive specimens were randomly selected and inoculated onto Madin-Darby Canine Kidney Epithelial cells (MDCK) for influenza virus isolation...
January 2017: Journal of Nepal Health Research Council
https://www.readbyqxmd.com/read/28711585/global-outbreak-of-severe-mycobacterium-chimaera-disease-after-cardiac-surgery-a-molecular-epidemiological-study
#6
Jakko van Ingen, Thomas A Kohl, Katharina Kranzer, Barbara Hasse, Peter M Keller, Anna Katarzyna Szafrańska, Doris Hillemann, Meera Chand, Peter Werner Schreiber, Rami Sommerstein, Christoph Berger, Michele Genoni, Christian Rüegg, Nicolas Troillet, Andreas F Widmer, Sören L Becker, Mathias Herrmann, Tim Eckmanns, Sebastian Haller, Christiane Höller, Sylvia B Debast, Maurice J Wolfhagen, Joost Hopman, Jan Kluytmans, Merel Langelaar, Daan W Notermans, Jaap Ten Oever, Peter van den Barselaar, Alexander B A Vonk, Margreet C Vos, Nada Ahmed, Timothy Brown, Derrick Crook, Theresa Lamagni, Nick Phin, E Grace Smith, Maria Zambon, Annerose Serr, Tim Götting, Winfried Ebner, Alexander Thürmer, Christian Utpatel, Cathrin Spröer, Boyke Bunk, Ulrich Nübel, Guido V Bloemberg, Erik C Böttger, Stefan Niemann, Dirk Wagner, Hugo Sax
BACKGROUND: Since 2013, over 100 cases of Mycobacterium chimaera prosthetic valve endocarditis and disseminated disease were notified in Europe and the USA, linked to contaminated heater-cooler units (HCUs) used during cardiac surgery. We did a molecular epidemiological investigation to establish the source of these patients' disease. METHODS: We included 24 M chimaera isolates from 21 cardiac surgery-related patients in Switzerland, Germany, the Netherlands, and the UK, 218 M chimaera isolates from various types of HCUs in hospitals, from LivaNova (formerly Sorin; London, UK) and Maquet (Rastatt, Germany) brand HCU production sites, and unrelated environmental sources and patients, as well as eight Mycobacterium intracellulare isolates...
July 12, 2017: Lancet Infectious Diseases
https://www.readbyqxmd.com/read/28710474/persistent-circulation-of-coxsackievirus-a6-of-genotype-d3-in-mainland-of-china-between-2008-and-2015
#7
Yang Song, Yong Zhang, Tianjiao Ji, Xinrui Gu, Qian Yang, Shuangli Zhu, Wen Xu, Yi Xu, Yong Shi, Xueyong Huang, Qi Li, Hong Deng, Xianjun Wang, Dongmei Yan, Wei Yu, Shuang Wang, Deshan Yu, Wenbo Xu
A total of 807 entire VP1 sequences of Coxsackievirus A6 (CV-A6) from mainland of China from 1992 to 2015, including 520 in this study and 287 from the GenBank database, were analysed to provide a basic framework of molecular epidemiological characteristics of CV-A6 in China. Sixty-five VP1 sequences including 46 representative CV-A6 isolates from 807 Chinese strains and 19 international strains from GenBank were used for describing the genotypes and sub-genotypes. The results revealed that CV-A6 strains can be categorised into 4 genotypes designated as A, B, C, and D according to previous data and can be further subdivided into B1-B2, C1-C2, and D1-D3 sub-genotypes...
July 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28710393/emergence-of-on1-genotype-of-human-respiratory-syncytial-virus-subgroup-a-in-china-between-2011-and-2015
#8
Jinhua Song, Yan Zhang, Huiling Wang, Jing Shi, Liwei Sun, Xiaojie Zhang, Zifeng Yang, Wenda Guan, Hong Zhang, Pengbo Yu, Zhengde Xie, Aili Cui, Teresa I Ng, Wenbo Xu
A molecular epidemiological study of human respiratory syncytial virus (HRSV) was conducted to examine the distribution of its subgroups and genotypes, as well as to identify its transmission pattern in China. A total of 705 samples collected from 9 provinces in China between January 2008 and February 2015 were identified as HRSV-positive and were subsequently sequenced. Of these, 336 samples were HRSV subgroup A (HRSVA), 368 samples were HRSV subgroup B (HRSVB), and 1 sample contained both HRSVA and HRSVB...
July 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28700322/molecular-epidemiology-of-avian-poxvirus-in-the-oriental-turtle-dove-streptopelia-orientalis-and-the-biting-midge-culicoides-arakawae-in-the-republic-of-korea
#9
Hae Rim Lee, Bon-Sang Koo, Jong-Taek Kim, Heung-Chul Kim, Myung-Soon Kim, Terry A Klein, Man-Seok Shin, Sanghun Lee, Eun-Ok Jeon, Kyung-Cheol Min, Seung Baek Lee, Yeonji Bae, In-Pil Mo
A total of 600 wild birds were analyzed for the causes of mortality in the Republic of Korea (ROK) from 2011 to 2013. Avian poxvirus (APV) infections were identified as the primary cause of mortality in 39% (29/74) Oriental Turtle Doves (Streptopelia orientalis). At necropsy, all 29 S. orientalis birds, of which, 76% (22/29) were juveniles, had severe diphtheritic lesions in their oral and nasal cavities and on their eyelids, which were the lesions of APV that resulted in mortality. We detected APV infection by chorioallantoic membrane inoculation and molecular study of the partial region of the P4b gene...
July 12, 2017: Journal of Wildlife Diseases
https://www.readbyqxmd.com/read/28698157/prevalence-molecular-epidemiology-and-zoonotic-potential-of-entamoeba-spp-in-nonhuman-primates-in-china
#10
Haiju Dong, Junqiang Li, Meng Qi, Rongjun Wang, Fuchang Yu, Fuchun Jian, Changshen Ning, Longxian Zhang
Amebiasis is a major public-health concern. It has a global distribution, and is listed as the third leading parasitic cause of human mortality. To survey the prevalence and assess the potential zoonotic transmission of Entamoeba spp. in nonhuman primates (NHPs) in China, 2688 fresh fecal specimens were collected from NHPs reared in farms or zoos/parks or free ranging in 13 districts. The overall prevalence of Entamoeba spp. infection determined with microscopy analysis was 39.4% (1059/2688). Higher infection rates were detected in the free ranging group (41...
July 8, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28697994/molecular-epidemiology-of-dientamoeba-fragilis
#11
REVIEW
Simone M Cacciò
The flagellated protozoan Dientamoeba fragilis is one of the most commonly diagnosed parasite of the human gut, with a global distribution. Nevertheless, essential aspects of its biology remain incompletely understood or controversial, most notably life cycle, host range, transmission routes and the ability to cause disease. Molecular epidemiologic studies are also scarce, and limited by the lack of informative genotyping tools. To date, two D. fragilis genotypes (1 and 2) are recognized, with a strong predominance of genotype 1 in both humans and few animal hosts...
July 8, 2017: Acta Tropica
https://www.readbyqxmd.com/read/28697828/-a-molecular-epidemiological-study-of-ki-polyomavirus-and-wu-polyomavirus-in-children-with-acute-respiratory-infection-in-tianjin-china
#12
Shu-Xiang Lin, Wei Wang, Wei Guo, Hong-Jiang Yang, Bai-Cheng Ma, Yu-Lian Fang, Yong-Sheng Xu
OBJECTIVE: To investigate the relationship of KI polyomavirus (KIPyV) and WU polyomavirus (WUPyV) with acute respiratory infection in children in Tianjin, China. METHODS: A total of 3 730 nasopharyngeal secretions were collected from hospitalized children with acute respiratory infection in Tianjin Children's Hospital from January 2011 to December 2013. Viral nucleic acid was extracted, and virus infection (KIPyV and WUPyV) was determined by PCR. Some KIPyV-positive and WUPyV-positive PCR products were subjected to sequencing...
July 2017: Zhongguo Dang Dai Er Ke za Zhi, Chinese Journal of Contemporary Pediatrics
https://www.readbyqxmd.com/read/28693301/serological-and-molecular-epidemiology-of-japanese-encephalitis-virus-infections-in-swine-herds-in-china-2006-2012
#13
Chunxia Chai, Qiao Wang, Sanjie Cao, Qin Zhao, Yiping Wen, Xiaobo Huang, Xintian Wen, Qiguai Yan, Xiaoping Ma, Rui Wu
Japanese encephalitis virus (JEV) is a mosquito-borne, zoonotic flavivirus causing viral encephalitis in humans and reproductive disorder in pig. JEV is widely prevalent throughout China in human, however, studies on JEV spatiotemporal analysis in Chinese swine herds have not been explored. Here, we present our serological and molecular epidemiological findings of the prevalence of JEV infections among swine herds in China, which suggest that JEV infections are extensively widespread and genotype I and III strains co-exist...
July 10, 2017: Journal of Veterinary Science
https://www.readbyqxmd.com/read/28692823/high-hiv-infection-prevalence-in-a-group-of-men-who-have-sex-with-men-msm
#14
Raquel Maria Cardoso Torres, Marly Marques da Cruz, André Reynaldo Santos Périssé, Denise Ribeiro Franqueira Pires
OBJECTIVE: To evaluate, by phenotypic and genotypic parameters, the presence of virulence and resistance factors in clinical Acinetobacter baumannii strains and verify the correlation between these variables. SETTINGS: Observational study conducted in an Universitary Hospital in Belo Horizonte, Brazil. METHODS: The confirmation of A. baumannii-calcoaceticus complex was performed by blaOXA51 detection, through the polymerase chain reaction (PCR) multiplex, as well as to investigate the presence of other oxacillinases (blaOXA23, 24, 58)...
July 7, 2017: Brazilian Journal of Infectious Diseases
https://www.readbyqxmd.com/read/28689232/co-circulation-of-three-clusters-of-793-b-like-avian-infectious-bronchitis-virus-genotypes-in-iranian-chicken-flocks
#15
Ali Yousefzadeh Kalokhoran, Arash Ghalyanchilangeroudi, Hossein Hosseini, Omid Madadgar, Vahid Karimi, Masoud Hashemzadeh, Parvaneh Hesari, Mohammad Taha Zabihi Petroudi, Hamideh Najafi
Avian infectious bronchitis (IB) is an acute and highly contagious viral disease causing severe economic losses in the poultry industry. The 793/B IB virus is an important infectious bronchitis virus (IBV) genotype currently circulating in several countries, including Iran. One hundred confirmed IBV samples (between 2014 and 2015; from 15 provinces in Iran) were selected for genotyping based on S1 sequencing. After phylogenetic analysis, it was found that 30% of the IBV isolates belonged to the 793/B genotype...
July 8, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28686503/characterization-of-carbapenem-resistant-escherichia-coli-isolates-through-the-whole-genome-sequencing-analysis
#16
Yanping Luo, Rong Luo, Hong Ding, Xiu Ren, Haipeng Luo, Ying Zhang, Liyan Ye, Shenghui Cui
Limited studies have characterized multiple carbapenem-resistant Escherichia coli isolates and compared their genetic characteristics through whole-genome sequencing (WGS) because of the scarcity of these isolates. In this study, we determined the prevalence of carbapenem resistance in 2,993 E. coli isolates collected from three Chinese hospitals. The carbapenem-resistant isolates were further characterized by WGS, and the molecular epidemiological characters and resistance mechanisms were explored through the publicly available platforms from the Center for Genomic Epidemiology...
July 7, 2017: Microbial Drug Resistance: MDR: Mechanisms, Epidemiology, and Disease
https://www.readbyqxmd.com/read/28684708/porcine-epidemic-diarrhea-in-europe-in-detail-analyses-of-disease-dynamics-and-molecular-epidemiology
#17
Dennis Hanke, Anne Pohlmann, Carola Sauter-Louis, Dirk Höper, Julia Stadler, Mathias Ritzmann, Adi Steinrigl, Bernd-Andreas Schwarz, Valerij Akimkin, Robert Fux, Sandra Blome, Martin Beer
Porcine epidemic diarrhea (PED) is an acute and highly contagious enteric disease of swine caused by the eponymous virus (PEDV) which belongs to the genus Alphacoronavirus within the Coronaviridae virus family. Following the disastrous outbreaks in Asia and the United States, PEDV has been detected also in Europe. In order to better understand the overall situation, the molecular epidemiology, and factors that might influence the most variable disease impact; 40 samples from swine feces were collected from different PED outbreaks in Germany and other European countries and sequenced by shot-gun next-generation sequencing...
July 6, 2017: Viruses
https://www.readbyqxmd.com/read/28683841/variable-expression-of-molecular-markers-in-juvenile-nasopharyngeal-angiofibroma
#18
A Mishra, A Pandey, S C Mishra
BACKGROUND: Molecular categorisation may explain the wide variation in the clinical characteristics of juvenile nasopharyngeal angiofibroma. METHODS: Variations in molecular markers in juvenile nasopharyngeal angiofibroma in an Indian population were investigated and compared with global reports. RESULTS: Variable molecular marker expression was demonstrated at the regional and global levels. A wide variation in molecular characteristics is evident...
July 7, 2017: Journal of Laryngology and Otology
https://www.readbyqxmd.com/read/28680043/molecular-epidemiology-of-mycobacterium-bovis-in-cameroon
#19
N F Egbe, A Muwonge, L Ndip, R F Kelly, M Sander, V Tanya, V Ngu Ngwa, I G Handel, A Novak, R Ngandalo, S Mazeri, K L Morgan, A Asuquo, B M de C Bronsvoort
We describe the largest molecular epidemiological study of Bovine Tuberculosis (bTB) in a sub-Saharan African country with higher spatial resolution providing new insights into bTB. Four hundred and ninety-nine samples were collected for culture from 201 and 179 cattle with and without bTB-like lesions respectively out of 2,346 cattle slaughtered at Bamenda, Ngaoundere, Garoua and Maroua abattoirs between 2012-2013. Two hundred and fifty-five M. bovis were isolated, identified and genotyped using deletion analysis, Hain® Genotype MTBC, spoligotyping and MIRU-VNTR...
July 5, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28679543/tracing-genetic-exchange-and-biogeography-of-cryptococcus-neoformans-var-grubii-at-the-global-population-level
#20
Johanna Rhodes, Christopher A Desjardins, Sean M Sykes, Mathew A Beale, Mathieu Vanhove, Sharadha Sakthikumar, Yuan Chen, Sharvari Gujja, Sakina Saif, Anuradha Chowdhary, Daniel John Lawson, Vinicius Ponzio, Arnaldo Lopes Colombo, Wieland Meyer, David M Engelthaler, Ferry Hagen, Maria Teresa Illnait-Zaragozi, Alexandre Alanio, Jo-Marie Vreulink, Joseph Heitman, John R Perfect, Anastasia Litvintseva, Tihana Bicanic, Thomas S Harrison, Matthew C Fisher, Christina A Cuomo
Cryptococcus neoformans var. grubii is the causative agent of cryptococcal meningitis, a significant source of mortality in immunocompromised individuals, typically HIV/AIDS patients from developing countries. Despite the worldwide emergence of this ubiquitous infection, little is known about the global molecular epidemiology of this fungal pathogen. Here we sequence the genomes of 188 diverse isolates and characterized the major subdivisions, their relative diversity and the level of genetic exchange between them...
July 5, 2017: Genetics
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