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Molecular-epidemiology

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https://www.readbyqxmd.com/read/29341983/diarrheagenic-escherichia-coli-and-acute-gastroenteritis-in-children-in-davidson-county-tennessee-united-states-a-case-control-study
#1
Aamer Imdad, Monique A Foster, Junaid Iqbal, Christopher Fonnesbeck, Daniel C Payne, Chengxian Zhang, James D Chappell, Natasha Halasa, Oscar G Gómez-Duarte
BACKGROUND: Diarrheagenic Escherichia coli (DEC) are an important cause of acute gastroenteritis in children; however, there is limited information available on the epidemiology, phylogenetics, serotyping, and antibiotic susceptibility of DEC in children in the United States. The aim of this study was to determine the molecular epidemiology of DEC among children with and without acute gastroenteritis in Davidson County, Tennessee. METHODS: This prospective, frequency matched, case-control study recruited subjects 15 days to 17 years of age and detected DEC with polymerase chain reaction from stool samples...
January 16, 2018: Pediatric Infectious Disease Journal
https://www.readbyqxmd.com/read/29339468/molecular-epidemiology-reveals-the-role-of-war-in-the-spread-of-hiv-in-ukraine
#2
Tetyana I Vasylyeva, Mariia Liulchuk, Samuel R Friedman, Iana Sazonova, Nuno R Faria, Aris Katzourakis, Nataliia Babii, Alla Scherbinska, Julien Thézé, Oliver G Pybus, Pavlo Smyrnov, Jean L Mbisa, Dimitrios Paraskevis, Angelos Hatzakis, Gkikas Magiorkinis
Ukraine has one of the largest HIV epidemics in Europe, historically driven by people who inject drugs (PWID). The epidemic showed signs of stabilization in 2012, but the recent war in eastern Ukraine may be reigniting virus spread. We investigated the movement of HIV-infected people within Ukraine before and during the conflict. We analyzed HIV-1 subtype-A pol nucleotide sequences sampled during 2012-2015 from 427 patients of 24 regional AIDS centers and used phylogeographic analysis to reconstruct virus movement among different locations in Ukraine...
January 16, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29339008/updates-on-the-molecular-epidemiology-of-enterovirus-d68-after-installation-of-screening-test-among-acute-flaccid-paralysis-patients-in-taiwan
#3
Hsin-Yi Wei, Ting-Kai Yeh, Juo-Yu Hsieh, I-Ping Lin, Jyh-Yuan Yang
In respond to acute flaccid paralysis (AFP) in association with Enterovirus D68 (EV-D68) infection, Taiwan Centers for Disease Control began to screen EV-D68 infection among each AFP patient since July 2015 and detected the first case in August 2016. This article updated the molecular epidemiology trends of EV-D68 from the national surveillance data.
January 3, 2018: Journal of Microbiology, Immunology, and Infection, Wei Mian Yu Gan Ran za Zhi
https://www.readbyqxmd.com/read/29334710/-a-study-on-genotype-of-271-mycobacterium-tuberculosis-isolates-in-6-prefectures-in-yunnan-province
#4
L Y Chen, X Yang, H H Ru, H J Yang, S Q Yan, L Ma, J O Chen, R Yang, L Xu
Objective: To understand the characteristics of genotypes of Mycobacterium tuberculosis isolates in Yunnan province, and provide the molecular epidemiological evidence for prevention and control of tuberculosis in Yunnan Province. Methods: Mycobacterium Tuberculosis isolates were collected from 6 prefectures of Yunnan province in 2014 and their Genetypes of Mycobacterium tuberculosis isolates were obtained using spoligotyping and multiple locus variable numbers of tandem repeats analysis (MLVA). The results of spoligotyping were entered into the SITVITWEB database to obtain the Spoligotyping International Type (SIT) patterns and the sublineages of MTB isolates...
January 6, 2018: Zhonghua Yu Fang Yi Xue za Zhi [Chinese Journal of Preventive Medicine]
https://www.readbyqxmd.com/read/29334709/-molecular-epidemiological-study-of-human-coronavirus-oc43-in-shanghai-from-2009-2016
#5
Y J Yang, Y W Hu
Objective: To understand the epidemiological characteristics of Human coronavirus (HCoV), the patterns of emergence and circulation, and the genotype distribution of human coronavirus OC43 (HCoV-OC43) from November, 2009 to April, 2016 in Shanghai. Methods: A total of 6 059 respiratory specimens, including pharyngeal swab, sputum, nasopharyngeal aspirates and alveolar lavage fluid, as well as relative clinical data were collected from patients with acute respiratory infections from seven sentinel hospitals during November, 2009 to April, 2016 in Shanghai...
January 6, 2018: Zhonghua Yu Fang Yi Xue za Zhi [Chinese Journal of Preventive Medicine]
https://www.readbyqxmd.com/read/29326013/a-cluster-of-multidrug-resistant-mycobacterium-tuberculosis-among-patients-arriving-in-europe-from-the-horn-of-africa-a-molecular-epidemiological-study
#6
Timothy M Walker, Matthias Merker, Astrid M Knoblauch, Peter Helbling, Otto D Schoch, Marieke J van der Werf, Katharina Kranzer, Lena Fiebig, Stefan Kröger, Walter Haas, Harald Hoffmann, Alexander Indra, Adrian Egli, Daniela M Cirillo, Jérôme Robert, Thomas R Rogers, Ramona Groenheit, Anne T Mengshoel, Vanessa Mathys, Marjo Haanperä, Dick van Soolingen, Stefan Niemann, Erik C Böttger, Peter M Keller
BACKGROUND: The risk of tuberculosis outbreaks among people fleeing hardship for refuge in Europe is heightened. We describe the cross-border European response to an outbreak of multidrug-resistant tuberculosis among patients from the Horn of Africa and Sudan. METHODS: On April 29 and May 30, 2016, the Swiss and German National Mycobacterial Reference Laboratories independently triggered an outbreak investigation after four patients were diagnosed with multidrug-resistant tuberculosis...
January 8, 2018: Lancet Infectious Diseases
https://www.readbyqxmd.com/read/29325865/emerging-discrepancies-in-conventional-and-molecular-epidemiology-of-methicillin-resistant-staph-aureus-isolated-from-bovine-milk
#7
Amjad Islam Aqib, Muhammad Ijaz, Shahid Hussain Farooqi, Rais Ahmed, Muhammad Shoaib, Muhammad Muddassir Ali, Khalid Mehmood, Hui Zhang
Methicillin resistant Staph aureus (MRSA) is an emerging public health concern from dairy milk, and its diagnosis by phenotypic methodology is experiencing higher discrepancies. The present study was planned to estimate discrepancies in phenotypic identification of MRSA and MSSA (Methicillin sensitive Staph aureus) in relation to mecA, and prevalent risk factors from various localities. In-vitro oxacilline antibiotic disks were used for phenotypic identification of MRSA, whereas mecA gene was used as MRSA marker in Staph aureus by PCR...
January 8, 2018: Microbial Pathogenesis
https://www.readbyqxmd.com/read/29325009/efficient-generation-of-complete-sequences-of-mdr-encoding-plasmids-by-rapid-assembly-of-minion-barcoding-sequencing-data
#8
Ruichao Li, Miaomiao Xie, Ning Dong, Dachuan Lin, Xuemei Yang, Marcus Ho Yin Wong, Edward Wai-Chi Chan, Sheng Chen
Background: Multidrug resistance (MDR)-encoding plasmids are considered major molecular vehicles responsible for transmission of antibiotic resistance genes among bacteria of the same or different species. Delineating the complete sequences of such plasmids could provide valuable insight into the evolution and transmission mechanisms underlying bacterial antibiotic resistance development. However, due to the presence of multiple repeats of mobile elements, complete sequencing of MDR plasmids remains technically complicated, expensive and time-consuming...
January 9, 2018: GigaScience
https://www.readbyqxmd.com/read/29324778/genetic-diversity-and-recombination-of-enterovirus-g-strains-in-japanese-pigs-high-prevalence-of-strains-carrying-a-papain-like-cysteine-protease-sequence-in-the-enterovirus-g-population
#9
Shinobu Tsuchiaka, Yuki Naoi, Ryo Imai, Tsuneyuki Masuda, Mika Ito, Masataka Akagami, Yoshinao Ouchi, Kazuo Ishii, Shoichi Sakaguchi, Tsutomu Omatsu, Yukie Katayama, Mami Oba, Junsuke Shirai, Yuki Satani, Yasuhiro Takashima, Yuji Taniguchi, Masaki Takasu, Hiroo Madarame, Fujiko Sunaga, Hiroshi Aoki, Shinji Makino, Tetsuya Mizutani, Makoto Nagai
To study the genetic diversity of enterovirus G (EV-G) among Japanese pigs, metagenomics sequencing was performed on fecal samples from pigs with or without diarrhea, collected between 2014 and 2016. Fifty-nine EV-G sequences, which were >5,000 nucleotides long, were obtained. By complete VP1 sequence analysis, Japanese EV-G isolates were classified into G1 (17 strains), G2 (four strains), G3 (22 strains), G4 (two strains), G6 (two strains), G9 (six strains), G10 (five strains), and a new genotype (one strain)...
2018: PloS One
https://www.readbyqxmd.com/read/29324747/association-of-atrial-fibrillation-and-cancer-analysis-from-two-large-population-based-case-control-studies
#10
Walid Saliba, Hedy S Rennert, Naomi Gronich, Stephen B Gruber, Gad Rennert
BACKGROUND: An association between atrial fibrillation (AF) and risk of cancer has been suggested in several studies, including prospective cohort studies. However, the magnitude and the temporal nature of this association remain unclear. METHODS: Data from two large prospective population-based case-control studies, the Molecular Epidemiology of Colorectal Cancer (MECC, n = 8,383) and the Breast Cancer in Northern Israel Study (BCINIS, n = 11,608), were used to better understand the nature and temporality of a possible association between cancer diagnosis and AF events before and after cancer diagnosis...
2018: PloS One
https://www.readbyqxmd.com/read/29319603/population-neuroscience-dementia-epidemiology-serving-precision-medicine-and-population-health
#11
Mary Ganguli, Emiliano Albanese, Sudha Seshadri, David A Bennett, Constantine Lyketsos, Walter A Kukull, Ingmar Skoog, Hugh C Hendrie
Over recent decades, epidemiology has made significant contributions to our understanding of dementia, translating scientific discoveries into population health. Here, we propose reframing dementia epidemiology as "population neuroscience," blending techniques and models from contemporary neuroscience with those of epidemiology and biostatistics. On the basis of emerging evidence and newer paradigms and methods, population neuroscience will minimize the bias typical of traditional clinical research, identify the relatively homogenous subgroups that comprise the general population, and investigate broader and denser phenotypes of dementia and cognitive impairment...
January 9, 2018: Alzheimer Disease and Associated Disorders
https://www.readbyqxmd.com/read/29318987/determination-of-trichomonas-vaginalis-genotypes-using-pcr-restriction-fragment-length-polymorphism-rflp
#12
Serpil Demirağ, Erdoğan Malatyalı, Sema Ertuğ, Hatice Ertabaklar
OBJECTIVE: Trichomonas vaginalis is an anaerobic protozoon and the most common non-viral sexually transmitted pathogen. The present study was designed to determine the genotypes of T. vaginalis using polymerase chain reaction (PCR)-restriction fragment length polymorphism of actin gene. METHODS: A total of 20 isolates from symptomatic females isolated and cryopreserved at Adnan Menderes University, Research and Training Hospital Parasitology Laboratory were included...
December 2017: Türkiye Parazitolojii Dergisi
https://www.readbyqxmd.com/read/29315661/what-is-changed-in-hbv-molecular-epidemiology-in-italy
#13
REVIEW
Alessia Lai, Caterina Sagnelli, Alessandra Lo Presti, Eleonora Cella, Silvia Angeletti, Silvia Spoto, Sebastiano Costantino, Evangelista Sagnelli, Massimo Ciccozzi
Hepatitis B virus (HBV) infection represents the most common cause of chronic liver diseases worldwide. Consequently, to the introduction of the universal HBV vaccination program, the prevalence of hepatitis B surface antigen was markedly reduced and less than 1% of the population of Western Europe and North America is chronically infected. To date, despite great advances in therapeutics, HBV chronic infection is considered an incurable disease. Ten hepatitis B virus genotypes (A-J) and several subgenotypes have been identified so far, based on intergroup divergences of 8% and 4%, respectively, in the complete viral genome...
January 9, 2018: Journal of Medical Virology
https://www.readbyqxmd.com/read/29315631/molecular-epidemiology-and-genotype-distributions-of-noroviruses-and-sapoviruses-in-thailand-2000-2016-a-review
#14
REVIEW
Kattareeya Kumthip, Pattara Khamrin, Niwat Maneekarn
Norovirus (NoV) and sapovirus (SaV) infections remain public health problems in Thailand, particularly, causing an acute gastroenteritis in people of all age groups. This review summarizes the epidemiology and genotype distribution of NoV and SaV in Thailand during the period of 2000 to 2016. The overall prevalence of NoV infection in patients with acute gastroenteritis of all age groups ranged from 0.09 to 44.7% while those of SaV were 0.0 to 15.0%. The majority of NoV genogroup detected was NoV GII with a small proportion of NoV GI...
January 5, 2018: Journal of Medical Virology
https://www.readbyqxmd.com/read/29314679/molecular-epidemiology-of-trichophyton-quinckeanum-a-zoophilic-dermatophyte-on-the-rise
#15
Silke Uhrlaß, Wieland Schroedl, Carolin Mehlhorn, Constanze Krüger, Vit Hubka, Thomas Maier, Yvonne Gräser, Uwe Paasch, Pietro Nenoff
BACKGROUND: Formerly only referred to as a subspecies (T. mentagrophytes var. quinckeanum), T. quinckeanum once again constitutes a distinct species according to the updated taxonomy of dermatophytes. PATIENTS AND METHODS: During routine diagnostic tests conducted at the Mycology Laboratory, Mölbis, Germany, between 11/2013 to 1/2017 (three years and three months), all specimens sent in were examined for T. quinckeanum. Molecular biology methods employed included: 1) DNA hybridization (PCR ELISA), 2) gene sequencing of the ITS region and TEF-1α, and 3) in some cases, MALDI-TOF mass spectrometry...
January 2018: Journal der Deutschen Dermatologischen Gesellschaft, Journal of the German Society of Dermatology: JDDG
https://www.readbyqxmd.com/read/29313468/molecular-epidemiology-of-an-orientia-tsutsugamushi-gene-encoding-a-56-kda-type-specific-antigen-in-chiggers-small-mammals-and-patients-from-the-southwest-region-of-korea
#16
Jung Wook Park, Sun Hee Kim, Duck Woong Park, So Hyang Jung, Hye Jung Park, Mi Hee Seo, Hyeon Je Song, Jung Yoon Lee, Dong Min Kim, Choon Mi Kim, Byong Chul Gill, Hang Jin Jeong, Jeong Min Lee, Dong Ryong Ha, Eun Sun Kim, Jae Keun Chung
A phylogenetic analysis of Orientia tsutsugamushi was performed to elucidate its antigenic diversity in chiggers, small mammals, and patients. Between September 2014 and December 2016, a total of 3,816 chiggers were identified within nine species of four genera in the southwest region of Korea: Leptotrombidium scutellare (49.9%; 1,907/3,816), Leptotrombidium orientale (21.1%; 804/3,816), Leptotrombidium pallidum (12.4%; 474/3,816), Euchoengastia koreaensis (7.2%; 273/3,816), Leptotrombidium palpale (6.7%; 256/3,816), Neotrombicular gardellai (1...
January 8, 2018: American Journal of Tropical Medicine and Hygiene
https://www.readbyqxmd.com/read/29311089/molecular-characterization-of-imp-1-producing-enterobacter-cloacae-complex-isolates-in-tokyo
#17
Kotaro Aoki, Sohei Harada, Koji Yahara, Yoshikazu Ishii, Daisuke Motooka, Shota Nakamura, Yukihiro Akeda, Tetsuya Iida, Kazunori Tomono, Satoshi Iwata, Kyoji Moriya, Kazuhiro Tateda
Although KPC enzymes are most common among carbapenemases produced by Enterobacter cloacae complex globally, the epidemiology varies from one country to another. While previous studies have suggested that IMP enzymes are most common in Japan, detailed analysis has been scarce thus far. Here we carried out a molecular epidemiological study and plasmid analysis of IMP-1-producing E. cloacae complex isolates collected from 3 hospitals in central Tokyo using whole genome sequencing. Seventy-one isolates were classified into several STs and 49 isolates were identified as Enterobacter hormaechei ST78...
January 8, 2018: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/29311074/molecular-epidemiology-and-mechanism-of-sulbactam-resistance-in-acinetobacter-baumannii-isolates-with-diverse-genetic-background-in-china
#18
Yunxing Yang, Ying Fu, Peng Lan, Qingye Xu, Yan Jiang, Yan Chen, Zhi Ruan, Shujuan Ji, Xiaoting Hua, Yunsong Yu
Sulbactam is a plausible option for treating Acinetobacter infection because of its intrinsic antibacterial activity against the Acinetobacter genus, but the mechanisms of sulbactam resistance have not been studied fully in Acinetobacter baumannii In this study, a total of 2197 clinical A. baumannii isolates were collected from 27 provinces in China. Eighty-eight isolates with various minimal inhibitory concentrations (MICs) for sulbactam were selected based on their diverse clonality and underwent multilocus sequence typing, antimicrobial-susceptibility testing and resistance gene screening...
January 8, 2018: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/29311067/molecular-epidemiology-of-emerging-blaoxa-23-like-and-blaoxa-24-like-carrying-acinetobacter-baumannii-in-taiwan
#19
Shu-Chen Kuo, Wei-Cheng Huang, Tzu-Wen Huang, Hui-Ying Wang, Jui-Fen Lai, Te-Li Chen, Tsai-Ling Lauderdale
Carbapenem-resistant Acinetobacter baumannii (CRAB) has increased significantly in recent decade in Taiwan. This study investigated the molecular epidemiology of CRAB with focus on the mechanisms of resistance and spread in isolates with blaOXA-23-like or blaOXA-24-like All 555 CRAB isolates in our 2002-2010 multi-centered collection were tested for the presence of class A, B and D carbapenemase genes. All isolates with blaOXA-23-like or blaOXA-24-like were subjected to PFGE and 82 isolates (60 blaOXA-23-like and 22 blaOXA-24-like) were selected for MLST to determine sequence type (ST) and clonal group (CG), and detection of additional β-lactamase and aminoglycoside genes...
January 8, 2018: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/29305646/genetic-and-immunogenicity-analysis-of-porcine-circovirus-type-2-strains-isolated-in-central-china
#20
Chang Liu, Yunchao Liu, Hongying Chen, Hua Feng, Yumei Chen, Yinbiao Wang, Juan Wang, Dongmin Liu, Ruiguang Deng, Gaiping Zhang
Porcine circovirus type 2 (PCV2) is an economically important pathogen in domestic pigs and wild boars all around the world. To understand the molecular epidemiology of PCV2 strains circulating in central China and to provide a potential vaccine candidate strain, we analyzed the genetic variations of 46 PCV2 isolates circulating from 2009 to 2016 in Henan Province (24 detected in the field from 2009-2013 and 22 from 2013-2016) and evaluated the efficacy of an isolate as a vaccine candidate strain in a mouse model...
January 5, 2018: Archives of Virology
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