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Khaled R Alkharsah, Suriya Rehman, Fatimah Alkhamis, Amani Alnimr, Asim Diab, Amein K Al-Ali
BACKGROUND: Methicillin resistant Staphylococcus aureus (MRSA) constitutes a major global health concern causing hospital and community acquired infections. A wide diversity of MRSA genotypes are circulating in geographically related regions. Therefore understanding the molecular epidemiology of MRSA is fundamental to design control and clearance measures. METHODS: A total of 106 MRSA isolates from infection (51) and carrier colonization sites (55) are characterized genetically based on SCCmec and MLST genotyping methods in addition to detection of PVL, TSST-1 and enterotoxins...
March 15, 2018: Annals of Clinical Microbiology and Antimicrobials
Xiangpeng Chen, Baoping Xu, Jiayun Guo, Changchong Li, Shuhua An, Yunlian Zhou, Aihuan Chen, Li Deng, Zhou Fu, Yun Zhu, Chunyan Liu, Lili Xu, Wei Wang, Kunling Shen, Zhengde Xie
To identify the variations in fusion (F) protein gene of RSV in China, a molecular epidemiological study was conducted. A total of 553 RSV positive specimens were collected from 2338 pediatric patients hospitalized with community-acquired pneumonia during a multi-center study conducted during 2014-2016. A total of 252 samples (183 RSV A, 69 RSV B) were selected for F gene sequencing, and analyzed together with 142 F gene sequences downloaded from GenBank. The result showed that all the Chinese RSV A and RSV B strains could be divided respectively into three branches...
March 14, 2018: Scientific Reports
Nguyen Van Diep, Masuo Sueyoshi, Junzo Norimine, Takuya Hirai, Ohnmar Myint, Angeline Ping Ping Teh, Uda Zahli Izzati, Naoyuki Fuke, Ryoji Yamaguchi
BACKGROUND: Since late 2013, porcine epidemic diarrhea virus (PEDV) has reemerged in Japan and caused severe economic losses to the swine industry. Although PEDV vaccines have been used widely, the disease has swept rapidly across the county, and is commonly observed in PED-vaccinated farms, and has recurred in domestic herds. To better understand PEDVs responsible for the reemerging outbreaks in Japan, full-length spike (S), membrane (M), and nucleocapsid (N) genes of 45 PEDVs collected in Japan during 2013-2016, were sequenced and analyzed...
March 14, 2018: BMC Veterinary Research
Zofia Bakuła, Anna Brzostek, Paulina Borówka, Anna Żaczek, Izabela Szulc-Kiełbik, Agata Podpora, Paweł Parniewski, Dominik Strapagiel, Jarosław Dziadek, Małgorzata Proboszcz, Jacek Bielecki, Jakko van Ingen, Tomasz Jagielski
Molecular epidemiological studies of Mycobacterium kansasii are hampered by the lack of highly-discriminatory genotyping modalities. The purpose of this study was to design a new, high-resolution fingerprinting method for M. kansasii. Complete genome sequence of the M. kansasii ATCC 12478 reference strain was searched for satellite-like repetitive DNA elements comprising tandem repeats. A total of 24 variable-number tandem repeat (VNTR) loci were identified with potential discriminatory capacity. Of these, 17 were used to study polymorphism among 67 M...
March 13, 2018: Scientific Reports
Xueyong Zhang, Yingna Jian, Xiuping Li, Liqing Ma, Gabriele Karanis, Panagiotis Karanis
Cryptosporidium is one of the most important genera of intestinal zoonotic pathogens, which can infect various hosts and cause diarrhoea. There is little available information about the molecular characterisation and epidemiological prevalence of Cryptosporidium spp. in Microtus fuscus (Qinghai vole) and Ochotona curzoniae (wild plateau pika) in the Qinghai-Tibetan Plateau area of Qinghai Province, Northwest China. Therefore, the aim of this study was to determine Cryptosporidium species/genotypes and epidemiological prevalence in these mammals by detecting the SSU rRNA gene by PCR amplification...
March 12, 2018: Parasitology Research
Wei Cong, Long Chen, Xiao-Feng Shan, Ai-Dong Qian, Qing-Feng Meng
Until now, limited information on the molecular epidemiology and genotypes of Toxoplasma gondii infection in donkeys is available in China. Thus, the present study was conducted to characterize T. gondii genotypes in donkeys, intended for human consumption in Shandong province, eastern China. A total of 618 muscle tissue samples of donkeys was collected in Shandong province from January 2016 to August 2017 and were used to detect the T. gondii B1 gene by a semi-nested PCR, and the positive samples were genotyped at 10 nuclear loci (i...
March 9, 2018: Infection, Genetics and Evolution
Carole Ayoub Moubareck, Shaimaa F Mouftah, Tibor Pál, Akela Ghazawi, Dalal H Halat, Anju Nabi, Mouza A AlSharhan, Zulfa O AlDeesi, Christabel C Peters, Handan Celiloglu, Manjunath Sannegowda, Dolla K Sarkis, Ágnes Sonnevend
Few studies have addressed the molecular epidemiology of carbapenem resistant Enterobacteriaceae (CRE) isolates in the Arabian Peninsula, and such investigations have been missing from Dubai, a major economical, tourism and medical centre of the region. The antibiotic susceptibility, the carbapenemase type produced, and the clonality of 89 CRE strains isolated in five major Dubai hospitals in June 2015 - June 2016 were determined. Thirty three percent of the collection of 70 K. pneumoniae, 13 E. coli and 6 other Enterobacteriaceae were extremely drug resistant, 27% were resistant to colistin, and 4...
March 9, 2018: International Journal of Antimicrobial Agents
Simonetta Mattiucci, Paolo Cipriani, Arne Levsen, Michela Paoletti, Giuseppe Nascetti
This review addresses the biodiversity, biology, distribution, ecology, epidemiology, and consumer health significance of the so far known species of Anisakis, both in their natural hosts and in human accidental host populations, worldwide. These key aspects of the Anisakis species' biology are highlighted, since we consider them as main driving forces behind which most of the research in this field has been carried out over the past decade. From a public health perspective, the human disease caused by Anisakis species (anisakiasis) appears to be considerably underreported and underestimated in many countries or regions around the globe...
2018: Advances in Parasitology
Chuanxiang Tang, Min Cai, Lin Wang, Yaqiong Guo, Na Li, Yaoyu Feng, Lihua Xiao
BACKGROUND: Cattle are commonly infected with the microsporidian parasite Enterocytozoon bieneusi. Sequence characterization of E. bieneusi in these animals at the ribosomal internal transcribed spacer (ITS) locus had identified I, J and BEB4 as the dominant genotypes. However, current studies on E. bieneusi in dairy cattle are mostly on infection rates and genotype distribution. This study aims to examine the intragenotypic diversity within dominant E. bieneusi genotypes in pre-weaned dairy calves in Shanghai, China...
March 12, 2018: Parasites & Vectors
Xiaoying Xie, Xinlu Dai, Lijia Ni, Baiji Chen, Zhaofan Luo, Yandan Yao, Xiquan Wu, Hongyu Li, Songyin Huang
BACKGROUND: Medical laboratory staff are a high-risk population for colonization of Staphylococcus aureus (S. aureus) due to direct and dense contact with the pathogens; however, there is limited information about this colonization. This study sought to determine the prevalence and molecular characteristics of nasal colonization by S. aureus in medical laboratory staff in Guangzhou, southern China, and to compare the differences between microbiological laboratory (MLS) and non-microbiological laboratory (NMLS) staff...
March 12, 2018: BMC Infectious Diseases
Jian Sun, Huimin Zhang, Ya-Hong Liu, Youjun Feng
Antibiotic resistance has become a global public health priority. Polymyxins, a family of cationic polypeptide antibiotics, act as a final line of refuge against severe infections by Gram-negative pathogens with pan-drug resistance. Unfortunately, this last-resort antibiotic has been challenged by the emergence and global spread of mobilized colistin resistance determinants (mcr). Given the fact that it has triggered extensive concerns worldwide, we present here an updated view of MCR-like colistin resistance...
March 7, 2018: Trends in Microbiology
Giancarlo Ripabelli, Manuela Tamburro, Giuliana Guerrizio, Incoronata Fanelli, Romeo Flocco, Massimiliano Scutellà, Michela L Sammarco
Antimicrobial-resistant Klebsiella pneumoniae represent a global public health concern. K. pneumoniae strains isolated during 2010 and 2014-2016 within a single hospital of Molise Region, Central Italy, were analyzed testing antimicrobial susceptibility, clonality by pulsed-field gel electrophoresis (PFGE) and random amplified polymorphic DNA (RAPD)-PCR, and prevalence of carbapenem resistance genes by PCR. Forty isolates (23 wild-type in 2010 and 17 non-wild-type in 2014-2016) were collected from hospitalized patients (65...
March 9, 2018: Current Microbiology
Sidhartha Giri, R Priya Hemavathy, Rajesh Arumugam, Jeevan B Sherchand, Hlaing Myat Thu, Geethani Galagoda, Theingi Win Myat, Nihal Abeysinghe, Madhava Gunasekara, Navaratnasingam Janakan, Rahul Pradhan, Vinod Bura, Pushparanjan Wijesinghe, Gagandeep Kang
BACKGROUND: In Asia, rotavirus accounts for approximately 45% of admissions due to acute gastroenteritis in children <5 years, and causes about 145,000 deaths every year. We studied the distribution of rotavirus strains from Myanmar, Sri Lanka, and Nepal during 2009-2015. METHODS: Stool samples collected from children <5 years of age hospitalized with acute diarrhea in the three sites and positive for rotavirus antigen by enzyme immunoassay (EIA) were sent to the Christian Medical College, Vellore from 2009 to 2015...
March 5, 2018: Vaccine
Hamid Solgi, Farzad Badmasti, Christian G Giske, Shadi Aghamohammad, Fereshteh Shahcheraghi
Objectives: Despite the fact that the blaOXA-48 and blaNDM-1 genes have successfully disseminated among Klebsiella pneumoniae isolates worldwide, outbreaks remain unidentified in Iran. Here we examined the molecular epidemiology of 96 carbapenem-resistant K. pneumoniae recovered from an Iranian hospital. Methods: A total of 96 non-replicate carbapenem-resistant K. pneumoniae were recovered from clinical specimens in a university hospital. Detection of ESBLs and carbapenemases produced by studied strains was performed using PCR and DNA sequencing...
March 6, 2018: Journal of Antimicrobial Chemotherapy
Christina A Cuomo, Johanna Rhodes, Christopher A Desjardins
Cryptococcus species are the causative agents of cryptococcal meningitis, a significant source of mortality in immunocompromised individuals. Initial work on the molecular epidemiology of this fungal pathogen utilized genotyping approaches to describe the genetic diversity and biogeography of two species, Cryptococcus neoformans and Cryptococcus gattii. Whole genome sequencing of representatives of both species resulted in reference assemblies enabling a wide array of downstream studies and genomic resources...
2018: Memórias do Instituto Oswaldo Cruz
Casey L Dagnall, Lindsay M Morton, Belynda D Hicks, Shengchao Li, Weiyin Zhou, Eric Karlins, Kedest Teshome, Salma Chowdhury, Kerrie S Lashley, Joshua N Sampson, Leslie L Robison, Gregory T Armstrong, Smita Bhatia, Gretchen A Radloff, Stella M Davies, Margaret A Tucker, Meredith Yeager, Stephen J Chanock
BACKGROUND: The recommended genomic DNA input requirements for whole genome single nucleotide polymorphism microarrays can limit the scope of molecular epidemiological studies. We performed a large-scale evaluation of whole genome amplified DNA as input into high-density, whole-genome Illumina® Infinium® SNP microarray. RESULTS: Overall, 6622 DNA samples from 5970 individuals were obtained from three distinct biospecimen sources and genotyped using gDNA and/or wgaDNA inputs...
March 6, 2018: BMC Genomics
Erik M Volz, Stephane Le Vu, Oliver Ratmann, Anna Tostevin, David Dunn, Chloe Orkin, Siobhan O'Shea, Valerie Delpech, Alison Brown, Noel Gill, Christophe Fraser
Background: The impact of HIV pre-exposure prophylaxis (PrEP) depends on infections averted by protecting vulnerable individuals as well as infections averted by preventing transmission by those who would have been infected if not receiving PrEP. Analysis of HIV phylogenies reveals risk factors for transmission, which we examine as potential criteria for allocating PrEP. Methods: We analyzed 6912 HIV-1 partial pol sequences from men who have sex with men (MSM) in the United Kingdom combined with global reference sequences and patient-level metadata...
February 26, 2018: Journal of Infectious Diseases
Eleonora Cella, Elitsa N Golkocheva-Markova, Diljana Trandeva-Bankova, Giulia Gregori, Roberto Bruni, Stefania Taffon, Michele Equestre, Angela Costantino, Silvia Spoto, Melissa Curtis, Anna Rita Ciccaglione, Massimo Ciccozzi, Silvia Angeletti
The purpose of this study was to analyze sequences of hepatitis A virus (HAV) Ia and Ib genotypes from Bulgarian patients to investigate the molecular epidemiology of HAV genotype I during the years 2012 to 2014. Around 105 serum samples were collected by the Department of Virology of the National Center of Infectious and Parasitic Diseases in Bulgaria. The sequenced region encompassed the VP1/2A region of HAV genome. The sequences obtained from the samples were 103. For the phylogenetic analyses, 5 datasets were built to investigate the viral gene in/out flow among distinct HAV subpopulations in different geographic areas and to build a Bayesian dated tree, Bayesian phylogenetic and migration pattern analyses were performed...
January 2018: Medicine (Baltimore)
Mengistu Damitie, Zeleke Mekonnen, Tadesse Getahun, Dante Santiago, Luc Leyns
BACKGROUND: Giardia duodenalis is a species complex consisting of multiple genetically distinct assemblages. The species imposes a major public health crisis on developing countries. However, the molecular diversity, transmission dynamics and risk factors of the species in these countries are indeterminate. This study was conducted to determine the molecular epidemiology of G. duodenalis infection in asymptomatic individuals in Southern Ethiopia. METHODS: From March to June 2014, fresh stool samples were collected from 590 randomly selected individuals...
March 5, 2018: Infectious Diseases of Poverty
O Smibert, A K Aung, E Woolnough, G P Carter, M B Schultz, B P Howden, T Seemann, D Spelman, S McGloughlin, A Y Peleg
Few studies have utilized molecular epidemiological methods to study transmission links to clinical isolates in intensive care units. 94 multi-drug resistant organisms (MDRO) cultured from routine specimens from ICU patients over 13 weeks were stored (11 MRSA, 2 VRE and 81 Gram-negative bacteria). Medical staff personal mobile phones, departmental phones and ICU keyboards were swabbed and cultured for MDRO; MRSA was isolated from two phones. Environmental and patient isolates of the same genus were selected for whole genome sequencing...
March 1, 2018: Journal of Hospital Infection
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