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Molecular-epidemiology

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https://www.readbyqxmd.com/read/29150913/molecular-epidemiology-of-goat-pox-viruses
#1
P Roy, S Jaisree, S Balakrishnan, K Senthilkumar, R Mahaprabhu, A Mishra, B Maity, T K Ghosh, A P Karmakar
Goat pox disease outbreaks were observed in different places affecting Black Bengal Goats in West Bengal (WB) and Tellicherry, Vembur and non-descriptive breeds in Tamil Nadu (TN) causing severe lesions and mortality up to 30%. Clinical specimens from all the outbreaks were screened by polymerase chain reaction followed by restriction fragment length polymorphism (PCR-RFLP) and confirmed the diseases as Goat Pox. Virus isolation in Vero cell line was done with randomly selected ten samples, cytopathic effects (CPE) characterized by syncytia and intracytoplasmic inclusion bodies were observed after several blind passages...
November 18, 2017: Transboundary and Emerging Diseases
https://www.readbyqxmd.com/read/29150903/phylogenetic-and-genetic-variation-analyses-of-porcine-circovirus-type-2-isolated-from-china
#2
S Yang, S Yin, Y Shang, B Liu, L Yuan, M U Zafar Khan, X Liu, J Cai
Porcine circovirus type 2 (PCV2) is a causative agent of PCV2-associated disease, which is a growing problem in the swine industry worldwide. High nucleotide substitution occurs in the capsid (Cap) gene of PCV2, which allows the continuous evolution and the emergence of novel PCV2 strains. In this study, we sequenced 24 Chinese PCV2 strains collected from healthy and diseased pigs between 2013 and 2015. Analyses of the genome, Cap and phylogeny classified the 24 Chinese PCV2 strains as PCV-2a (four of 24), PCV-2b (five of 24) and PCV-2d (15 of 24)...
November 17, 2017: Transboundary and Emerging Diseases
https://www.readbyqxmd.com/read/29148521/author-s-correction-molecular-epidemiology-and-antimicrobial-susceptibility-of-ampc-and-or-extended-spectrum-esbl-%C3%A3-lactamaseproducing-proteus-spp-clinical-isolates-in-zenica-doboj-canton-bosnia-and-herzegovina
#3
Selma Uzunović, Amir Ibrahimagić, Branka Bedenić
Volume 13, no. 2, p. 103-112, 2016. Page 103: The byline should appear as shown above.
August 2017: Medicinski Glasnik
https://www.readbyqxmd.com/read/29146194/association-analyses-of-genetic-variants-in-long-non-coding-rna-malat1-with-breast-cancer-susceptibility-and-mrna-expression-of-malat1-in-chinese-han-population
#4
Rui Peng, Chenglin Luo, Qiaoyun Guo, Jingjing Cao, Qian Yang, Kaiyan Dong, Shuaibing Wang, Kaijuan Wang, Chunhua Song
The long non-coding RNA (lncRNA) Metastasis-associated lung adenocarcinoma transcript 1(MALAT1) has been implicated in breast cancer (BC). Polymorphisms in MALAT1 may play a vital role in the progress of breast cancer by its regulation function. However, potential genetic variants in MALAT1 affecting the development of BC is rarely explored. In our current molecular epidemiology study, all three tagging SNPs (rs3200401, rs619586 and rs7927113) in lncRNA MALAT1 were selected for genotyping in 487BCE patients and 489 cancer-free controls in Chinese Han population, and futher experiment of quantitative real-time (qRT) PCR was conducted to examine the relative expression of MALAT1...
November 13, 2017: Gene
https://www.readbyqxmd.com/read/29143492/molecular-epidemiological-survey-and-phylogenetic-analysis-of-bovine-influenza-d-virus-in-japan
#5
H Mekata, M Yamamoto, S Hamabe, H Tanaka, T Omatsu, T Mizutani, B M Hause, T Okabayashi
The influenza D virus, a new member of the Orthomyxoviridae family, is predominantly found in cattle. Although viral pathology and clinical disease in cattle appear mild, this virus plays an important role as a trigger of bovine respiratory disease (BRD). BRD is a costly illness worldwide. Thus, epidemiological surveys of the influenza D virus are necessary. Here, we conducted a molecular epidemiological survey for the influenza D virus in healthy and respiratory-diseased cattle in Japan. We found that 2.1% (8/377) of the cattle were infected with influenza D...
November 16, 2017: Transboundary and Emerging Diseases
https://www.readbyqxmd.com/read/29141348/-molecular-epidemiology-and-transmission-of-hiv-1-infection-in-zhejiang-province-2015
#6
J Z Yang, W J Chen, W J Zhang, L He, J F Zhang, X H Pan
Objective: To understand the distribution of HIV-1 subtype diversity and its transmission characteristics in Zhejiang province. Methods: A total of 302 newly diagnosed HIV-1 positive patients were selected through stratified random sampling in Zhejiang in 2015. HIV-1 pol genes were sequenced successfully with reverse transcription PCR/nested PCR and phylogenetic analysis was conducted for 276 patients. Then a molecular epidemiologic study was performed combined with field epidemiological investigation. Results: Of 276 sequence samples analyzed, 122 CRF07_BC strains (44...
November 10, 2017: Zhonghua Liu Xing Bing Xue za Zhi, Zhonghua Liuxingbingxue Zazhi
https://www.readbyqxmd.com/read/29141051/molecular-and-epidemiological-characterization-of-carbapenemase-producing-enterobacteriaceae-in-norway-2007-to-2014
#7
Ørjan Samuelsen, Søren Overballe-Petersen, Jørgen Vildershøj Bjørnholt, Sylvain Brisse, Michel Doumith, Neil Woodford, Katie L Hopkins, Bettina Aasnæs, Bjørg Haldorsen, Arnfinn Sundsfjord
The prevalence of carbapenemase-producing Enterobacteriaceae (CPE) is increasing worldwide. Here we present associated patient data and molecular, epidemiological and phenotypic characteristics of all CPE isolates in Norway from 2007 to 2014 confirmed at the Norwegian National Advisory Unit on Detection of Antimicrobial Resistance. All confirmed CPE isolates were characterized pheno- and genotypically, including by whole genome sequencing (WGS). Patient data were reviewed retrospectively. In total 59 CPE isolates were identified from 53 patients...
2017: PloS One
https://www.readbyqxmd.com/read/29140998/using-whole-genome-sequencing-to-study-american-foulbrood-epidemiology-in-honeybees
#8
Joakim Ågren, Marc Oliver Schäfer, Eva Forsgren
American foulbrood (AFB), caused by Paenibacillus larvae, is a devastating disease in honeybees. In most countries, the disease is controlled through compulsory burning of symptomatic colonies causing major economic losses in apiculture. The pathogen is endemic to honeybees world-wide and is readily transmitted via the movement of hive equipment or bees. Molecular epidemiology of AFB currently largely relies on placing isolates in one of four ERIC-genotypes. However, a more powerful alternative is multi-locus sequence typing (MLST) using whole-genome sequencing (WGS), which allows for high-resolution studies of disease outbreaks...
2017: PloS One
https://www.readbyqxmd.com/read/29137167/transmission-dynamics-of-hiv-1-drug-resistance-among-treatment-na%C3%A3-ve-individuals-in-greece-the-added-value-of-molecular-epidemiology-to-public-health
#9
Dimitrios Paraskevis, Evangelia Kostaki, Panagiotis Gargalianos, Georgios Xylomenos, Marios Lazanas, Maria Chini, Athanasios Skoutelis, Vasileios Papastamopoulos, Dimitra Paraskeva, Anastasia Antoniadou, Antonios Papadopoulos, Mina Psichogiou, Georgios L Daikos, Georgios Chrysos, Vasileios Paparizos, Sofia Kourkounti, Helen Sambatakou, Nikolaos V Sipsas, Malvina Lada, Periklis Panagopoulos, Efstratios Maltezos, Stylianos Drimis, Angelos Hatzakis
The presence of human immunodeficiency virus type 1 (HIV-1) drug resistance among drug-naïve patients remains stable, although the proportion of patients with virological failure to therapy is decreasing. The dynamics of transmitted resistance among drug-naïve patients remains largely unknown. The prevalence of non-nucleoside reverse transcriptase inhibitors (NNRTI) resistance was 16.9% among treatment-naïve individuals in Greece. We aimed to investigate the transmission dynamics and the effective reproductive number (Re) of the locally transmitted NNRTI resistance...
November 13, 2017: Genes
https://www.readbyqxmd.com/read/29136186/clonal-spread-and-azole-resistant-mechanisms-of-non-susceptible-candida-albicans-isolates-from-vulvovaginal-candidiasis-patients-in-three-shanghai-maternity-hospitals
#10
YongQin Wu, Cui Li, ZhiHeng Wang, Jing Gao, ZhenHua Tang, HuiFen Chen, ChunMei Ying
In our multicenter study, 43 fluconazole non-susceptible and 45 fluconazole-susceptible isolates were collected from vulvovaginal candidiasis (VVC) patients from three Shanghai maternity hospitals to analyze their molecular epidemiological features and fluconazole resistant mechanisms. Cross-resistance to fluconazole, itraconazole and voriconazole was observed in 53.5% of the nonsusceptible isolates. Though we acquired 12 clonal complexes (CCs) of diploid sequence types (DSTs) in clinical isolates by a multilocus sequence typing method, fluconazole nonsusceptible isolates all belonged to CC69 with a predominant genotype of DST 79...
November 9, 2017: Medical Mycology: Official Publication of the International Society for Human and Animal Mycology
https://www.readbyqxmd.com/read/29132926/molecular-epidemiology-of-%C3%AE-lactamase-production-in-penicillin-susceptible-staphylococcus-aureus-under-high-susceptibility-conditions
#11
Takashi Matono, Maki Nagashima, Kazuhisa Mezaki, Ayano Motohashi, Satoshi Kutsuna, Kayoko Hayakawa, Norio Ohmagari, Mitsuo Kaku
Little is known about the prevalence of β-lactamase production in penicillin-susceptible Staphylococcus aureus isolates under high-susceptibility conditions. We analyzed S. aureus isolates with penicillin G minimum inhibitory concentration (MIC) ≤ 0.12 μg/ml that were recovered from in-/outpatients (n = 108) between 2016 and 2017 in Japan. β-Lactamase production was detected by nitrocefin-based and Clinical and Laboratory Standards Institute penicillin zone edge testing and blaZ PCR. All isolates were categorized as having penicillin G MIC ≤0...
November 10, 2017: Journal of Infection and Chemotherapy: Official Journal of the Japan Society of Chemotherapy
https://www.readbyqxmd.com/read/29127047/heteroresistance-to-carbapenems-in-invasive-pseudomonas-aeruginosa-infections
#12
Jianchun He, Xiaojiong Jia, Shuangshuang Yang, Xiuyu Xu, Kunling Sun, Congya Li, Tianxiang Yang, Liping Zhang
Heteroresistance is not rare in a variety of microbes, but carbapenem heteroresistace (CHR) among invasive P. aeruginosa infections has not been thoroughly characterized to date. The objective of this study was to investigate the mechanisms, molecular epidemiology, and risk factors for invasive carbapenem heteroresistant P. aeruginosa (CHPA) infections between 2011 and 2015 in Chongqing, China. We observed a significant increase in rates of heteroresistance to IPM (IPM-HR) and MEM (MEM-HR) during the study period...
November 7, 2017: International Journal of Antimicrobial Agents
https://www.readbyqxmd.com/read/29125052/prevalence-of-extended-spectrum-beta-lactamase-and-carbapenemase-producing-bloodstream-isolates-of-klebsiella-pneumoniae-in-a-tertiary-care-hospital
#13
Henrietta Abodakpi, Kai-Tai Chang, Ana María Sánchez Díaz, Rafael Cantón, Todd M Lasco, Katrina Chan, Amelia K Sofjan, Vincent H Tam
To improve prescribing of empiric therapy, the local molecular epidemiology of extended-spectrum beta-lactamases (ESBLs) and Klebsiella pneumoniae carbapenemases (KPCs) in bloodstream isolates of K. pneumoniae were evaluated. Isolates resistant to third generation cephalosporins were screened phenotypically for ESBLs and carbapenemases, and subsequently confirmed by PCR for the presence of ESBL (blaTEM, blaSHV and blaCTX-M) and carbapenemase (blaKPC, blaVIM, blaNDM and blaOXA-48) genes. Hydrolytic activity (functional gene expression) was quantified using a nitrocefin degradation assay and correlated to ceftazidime or meropenem MIC...
November 10, 2017: Journal of Chemotherapy
https://www.readbyqxmd.com/read/29119691/the-detection-of-porcine-circovirus-3-in-guangxi-china
#14
S Wen, W Sun, Z Li, X Zhuang, G Zhao, C Xie, M Zheng, J Jing, P Xiao, M Wang, J Han, J Ren, H Liu, H Lu, N Jin
Porcine circovirus type 3 (PCV3) is a novel circovirus that was firstly detected in the USA. PCV3 is associated with porcine dermatitis and nephropathy syndrome (PDNS), reproductive failure and cardiac and multisystemic inflammation. Latterly, PCV3 was detected in Guangxi, China. Forty-one of 108 (37.96%) samples and nine of 47 (19.14%) samples were PCV3 positive in pig farms and pig slaughter houses, respectively. Three PCV3 strains were sequenced and designated PCV3-China/GX2016-1, PCV3-China/GX2016-2 and PCV3-China/GX2016-3...
November 8, 2017: Transboundary and Emerging Diseases
https://www.readbyqxmd.com/read/29116630/genomic-epidemiology-of-tuberculosis
#15
Iñaki Comas
The application of next generation sequencing technologies has opened the door to a new molecular epidemiology of tuberculosis, in which we can now look at transmission at a resolution not possible before. At the same time, new technical and analytical challenges have appeared, and we are still exploring the wider potential of this new technology. Whole genome sequencing in tuberculosis still requires bacterial cultures. Thus, although whole genome sequencing has revolutionized the interpretation of transmission patterns, it is not yet ready to be applied at the point-of-care...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/29116454/characterization-of-the-complete-mitochondrial-genome-of-marshallagia-marshalli-and-phylogenetic-implications-for-the-superfamily-trichostrongyloidea
#16
Miao-Miao Sun, Liang Han, Fu-Kai Zhang, Dong-Hui Zhou, Shu-Qing Wang, Jun Ma, Xing-Quan Zhu, Guo-Hua Liu
Marshallagia marshalli (Nematoda: Trichostrongylidae) infection can lead to serious parasitic gastroenteritis in sheep, goat, and wild ruminant, causing significant socioeconomic losses worldwide. Up to now, the study concerning the molecular biology of M. marshalli is limited. Herein, we sequenced the complete mitochondrial (mt) genome of M. marshalli and examined its phylogenetic relationship with selected members of the superfamily Trichostrongyloidea using Bayesian inference (BI) based on concatenated mt amino acid sequence datasets...
November 7, 2017: Parasitology Research
https://www.readbyqxmd.com/read/29111140/genomics-and-molecular-epidemiology-of-cryptosporidium-species
#17
REVIEW
Asis Khan, Jahangheer S Shaik, Michael E Grigg
Cryptosporidium is one of the most widespread protozoan parasites that infects domestic and wild animals and is considered the second major cause of diarrhea and death in children after rotavirus. So far, around 20 distinct species are known to cause severe to moderate infections in humans, of which Cryptosporidium hominis and Cryptosporidium parvum are the major causative agents. Currently, ssurRNA and gp60 are used as the optimal markers for differentiating species and subtypes respectively. Over the last decade, diagnostic tools to detect and differentiate Cryptosporidium species at the genotype and subtype level have improved, but our understanding of the zoonotic and anthroponotic transmission potential of each species is less clear, largely because of the paucity of high resolution whole genome sequencing data for the different species...
October 27, 2017: Acta Tropica
https://www.readbyqxmd.com/read/29107195/application-of-whole-genome-sequence-data-in-analyzing-the-molecular-epidemiology-of-shiga-toxin-producing-escherichia-coli-o157-h7-h
#18
Eiji Yokoyama, Shinichiro Hirai, Taichiro Ishige, Satoshi Murakami
Seventeen clusters of Shiga toxin-producing Escherichia coli O157:H7/- (O157) strains, determined by cluster analysis of pulsed-field gel electrophoresis patterns, were analyzed using whole genome sequence (WGS) data to investigate this pathogen's molecular epidemiology. The 17 clusters included 136 strains containing strains from nine outbreaks, with each outbreak caused by a single source contaminated with the organism, as shown by epidemiological contact surveys. WGS data of these strains were used to identify single nucleotide polymorphisms (SNPs) by two methods: short read data were directly mapped to a reference genome (mapping derived SNPs) and common SNPs between the mapping derived SNPs and SNPs in assembled data of short read data (common SNPs)...
October 17, 2017: International Journal of Food Microbiology
https://www.readbyqxmd.com/read/29103272/first-case-of-canine-infection-with-hepatozoon-canis-apicomplexa-haemogregarinidae-in-the-republic-of-korea
#19
Seung-Joo Kwon, Yoon-Hee Kim, Hyun-Hee Oh, Ul-Soo Choi
This report describes a dog infected with Hepatozoon canis, the first canine infection in the Republic of Korea. A 2-year-old intact male Maltese dog presented with anorexia and depression. Physical examinations revealed mild dehydration and hyperthermia (39.8°C), and blood analysis showed pancytopenia. Diff-Quik staining of blood smear specimens showed the presence of ellipsoidal shaped structures (gamonts of H. canis) within a small number of neutrophils. Real-time PCR analysis using whole blood confirmed infection by H...
October 2017: Korean Journal of Parasitology
https://www.readbyqxmd.com/read/29102115/molecular-epidemiology-of-swine-influenza-a-viruses-in-the-southeastern-united-states-highlights-regional-differences-in-circulating-strains
#20
Constantinos S Kyriakis, Ming Zhang, Stefan Wolf, Les P Jones, Byoung-Shik Shim, Anna H Chocallo, Jarod M Hanson, MingRui Jia, Dong Liu, Ralph A Tripp
Swine influenza A virus (IAV) can cause widespread respiratory disease with high morbidity, low mortality, and have a substantial economic impact to the swine industry. Swine infection may contribute to pandemic IAV given their susceptibility to both avian and human IAVs. Currently, three IAV subtypes (H1N1, H3N2 and H1N2) circulate in swine in North America frequently combining gene segments from avian or human viruses. This study investigated the prevalence of IAV in commercial swine herds. A total of 1878 oral fluid samples were collected from pigs of all ages from 201 commercial farms located in North Carolina and South Carolina...
November 2017: Veterinary Microbiology
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