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Rebekah M Martin, Jie Cao, Sylvain Brisse, Virginie Passet, Weisheng Wu, Lili Zhao, Preeti N Malani, Krishna Rao, Michael A Bachman
Klebsiella pneumoniae is among the most common causes of hospital-acquired infections and has emerged as an urgent threat to public health due to carbapenem antimicrobial resistance. K. pneumoniae commonly colonizes hospitalized patients and causes extraintestinal infections such as urinary tract infection, bloodstream infection (septicemia), and pneumonia. If colonization is an intermediate step before infection, then detection and characterization of colonizing isolates could enable strategies to prevent or empirically treat K...
September 2016: MSphere
José A L Fernandes, Tâmara H R Prandini, Maria da Conceiçao A Castro, Thales D Arantes, Juliana Giacobino, Eduardo Bagagli, Raquel C Theodoro
Inteins are invasive intervening sequences that perform an autocatalytic splicing from their host proteins. Among eukaryotes, these elements are present in many fungal species, including those considered opportunistic or primary pathogens, such as Candida spp. Here we reviewed and updated the list of Candida species containing inteins in the genes VMA, THRRS and GLT1 and pointed out the importance of these elements as molecular markers for molecular epidemiological researches and species-specific diagnosis, since the presence, as well as the size of these inteins, is polymorphic among the different species...
2016: Frontiers in Microbiology
Andrew Rambaut, Tommy T Lam, Luiz Max Carvalho, Oliver G Pybus
Gene sequences sampled at different points in time can be used to infer molecular phylogenies on a natural timescale of months or years, provided that the sequences in question undergo measurable amounts of evolutionary change between sampling times. Data sets with this property are termed heterochronous and have become increasingly common in several fields of biology, most notably the molecular epidemiology of rapidly evolving viruses. Here we introduce the cross-platform software tool, TempEst (formerly known as Path-O-Gen), for the visualization and analysis of temporally sampled sequence data...
January 2016: Virus Evolution
Marta Canuti, Kimberly E O'Leary, Bruce D Hunter, Grant Spearman, Davor Ojkic, Hugh G Whitney, Andrew S Lang
Aleutian mink disease virus (AMDV) causes plasmacytosis, an immune complex-associated syndrome that affects wild and farmed mink. The virus can also infect other small mammals (e.g., ferrets, skunks, ermines, and raccoons), but the disease in these hosts has been studied less. In 2007, a mink plasmacytosis outbreak began on the Island of Newfoundland, and the virus has been endemic in farms since then. In this study, we evaluated the molecular epidemiology of AMDV in farmed and wild animals of Newfoundland since before the beginning of the outbreak and investigated the epidemic in a global context by studying AMDV worldwide, thereby examining its diffusion and phylogeography...
January 2016: Virus Evolution
Matthew D Hall, Mark E J Woolhouse, Andrew Rambaut
The ongoing large-scale increase in the total amount of genetic data for viruses and other pathogens has led to a situation in which it is often not possible to include every available sequence in a phylogenetic analysis and expect the procedure to complete in reasonable computational time. This raises questions about how a set of sequences should be selected for analysis, particularly if the data are used to infer more than just the phylogenetic tree itself. The design of sampling strategies for molecular epidemiology has been a neglected field of research...
January 2016: Virus Evolution
Meripet Polat, Hla Hla Moe, Takeshi Shimogiri, Kyaw Kyaw Moe, Shin-Nosuke Takeshima, Yoko Aida
Bovine leukemia virus (BLV) is the etiological agent of enzootic bovine leukosis, which is the most common neoplastic disease of cattle. BLV infects cattle worldwide and affects both health status and productivity. However, no studies have examined the distribution of BLV in Myanmar, and the genetic characteristics of Myanmar BLV strains are unknown. Therefore, the aim of this study was to detect BLV infection in Myanmar and examine genetic variability. Blood samples were obtained from 66 cattle from different farms in four townships of the Nay Pyi Taw Union Territory of central Myanmar...
October 22, 2016: Archives of Virology
Fabrizio Anniballi, Silvia Fillo, Francesco Giordani, Bruna Auricchio, Domenico Azarnia Tehran, Enrica di Stefano, Giuseppina Mandarino, Dario De Medici, Florigio Lista
Clostridium botulinum is the bacterial agent of botulism, a rare but severe neuro-paralytic disease. Because of its high impact, in Italy botulism is monitored by an ad hoc surveillance system. The National Reference Centre for Botulism, as part of this system, collects and analyzes all demographic, epidemiologic, microbiological, and molecular data recovered during cases and/or outbreaks occurred in Italy. A panel of 312 C. botulinum strains belonging to group I were submitted to MLVA sub-typing. Strains, isolated from clinical specimens, food and environmental samples collected during the surveillance activities, were representative of all forms of botulism from all Italian regions...
October 19, 2016: Infection, Genetics and Evolution
Mostafa Ghanem, Mohamed El-Gazzar
Mycoplasma iowae (MI) infection is an economically and commercially important disease of turkeys. There are no sequence typing assays available for MI strain identification, the only available molecular tools for this purpose, are DNA fingerprinting assays. In addition to their low reproducibility, fingerprinting assays require isolation of the microorganism in pure culture, which is difficult for avian mycoplasma. Therefore, we propose a multilocus sequence typing (MLST) assay as the first genotyping assay for identification of MI...
November 15, 2016: Veterinary Microbiology
Aura Falco, Yusibeska Ramos, Esther Franco, Alegría Guzmán, Howard Takiff
BACKGROUND: Klebsiella pneumoniae is a bacterial pathogen that has developed resistance to multiple antibiotics and is a major cause of nosocomial infections worldwide. Carbapenemase-producing Klebsiella pneumoniae have been isolated in many hospitals in Venezuela, but they have not been well-studied. The aim of this study was to characterize carbapenem-resistant Klebsiella pneumoniae isolates from the pediatric service of a hospital located in Anzoategui State, in the eastern part of Venezuela...
October 22, 2016: BMC Infectious Diseases
Ananya Tupaki-Sreepurna, Abdullah M S Al-Hatmi, Anupma J Kindo, Murugan Sundaram, G Sybren de Hoog
In this study, we aimed to present the first molecular epidemiological data from Chennai, India, analyse keratitis cases that have been monitored in a university hospital during 2 years, identify the responsible Fusarium species and determine antifungal susceptibilities. A total of 10 cases of keratitis were included in the study. Fusarium isolates were identified using the second largest subunit of the RNA polymerase gene (RPB2) and the translation elongation factor 1 alpha (TEF1). Antifungal susceptibility was tested by the broth microdilution method according to the Clinical and Laboratory Standards Institute (CLSI) methodology...
October 21, 2016: Mycoses
Po-Liang Lu, Ya-Ju Hsieh, Jun-En Lin, Jun-Wei Huang, Tsung-Ying Yang, Lin Lin, Sung-Pin Tseng
Although fosfomycin is a treatment option for infections caused by extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae, fosfomycin resistance has been documented. To our knowledge, fosfomycin resistance mechanisms in Klebsiella pneumoniae have not been systematically investigated. A total of 108 ESBL-producing K. pneumoniae isolates collected from Kaohsiung Medical University Hospital, Taiwan, from August 2012 to May 2013 were analysed in this study. Pulsed-field gel electrophoresis (PFGE) revealed 64 pulsotypes and six non-typeable isolates, indicating high genetic diversity...
September 30, 2016: International Journal of Antimicrobial Agents
Ahmed Abdel Megeed, M Ali Hayssam, Mohamed Z M Salem, Mohamed S El-Shikh, Ibrahim Ahmed Talea, Yahya A Alogaibi
Multidrug-resistant (MDR) Acinetobacter baumannii infections are a great public health concern and demand continuous surveillance and antibiotic stewardship. Virulence traits and the pathogenicity of Acinetobacter are less studied compared with the molecular epidemiological and antibiotic resistance profile of this organism. In our present study, we investigated the primary characteristics contributing to the virulence of MDR A. baumannii isolates and compared them with avirulent isolates. A total of 32 well-characterized MDR A...
October 19, 2016: Journal of AOAC International
Wenjun Zhang, Junfang Chen, Xiao Hong Pan, Jiafeng Zhang, Zhihong Guo, Yan Luo, Jiezhe Yang, Yan Xia, Lin He, Yun Xu, Ke Xu, Xiaobei Ding
OBJECTIVE: To investigate the HIV-1 molecular epidemiology among young people (18 to 25 years old) in Hangzhou. METHODS: Plasma samples from 262 newly diagnosed HIV-1 infected patients were collected between 2009 and 2013 from Hangzhou of Zhejiang province. HIV-1 nucleotide sequences of pol gene regions were amplified using a nested PCR method and sequenced. Phylogenetic and recombination analyses were used to determine the HIV-1 genotypes. RESULTS: Based on all sequences generated, the subtype/circulating recombinant forms (CRF) distribution was as follows: CRF01_AE (68...
October 20, 2016: AIDS Research and Human Retroviruses
Yihong Hu, Zhenzhou Wan, Yan-Heng Zhou, Davey M Smith, Yong-Tang Zheng, Chiyu Zhang
The on-going generation of HIV-1 inter-subtype recombination has led to new circulating recombinant forms (CRFs) and unique recombinant forms (URFs) in Asia. Here, we evaluated whether previously reported URFs were actually CRFs. All available complete or near full-length HIV-1 URFs sequences from Asia were retrieved from the HIV Los Alamos National Laboratory Sequence database, and phylogenetic, transmission cluster and bootscan analyses were performed using MEGA 6.0, Cluster Picker 1.2.1, and SimPlot3.5.1...
October 20, 2016: AIDS Research and Human Retroviruses
Zhonglan Wu, Lijia Cui, Weiming Zhao, Dongzhi Yang, Hui Chen, Ruiqing Wang, Xuemin Wang, Linqi Zhang, Tianhua He
BACKGROUND: Current prevalence and genotype distribution of hepatitis C virus (HCV) infection remain unknown in Ningxia, northwest China. METHODS: From June to December 2013, 13,022 individuals were screened in Ningxia HIV/AIDS Sentinel Surveillance System, with their demographic features collected and serum samples tested for HCV antibody. Sero-positive drug users were further subjected to sequencing of NS5B and Core regions of HCV. RESULTS: The anti-HCV prevalence was 0...
October 18, 2016: Virology Journal
Cecilia Olguin Perglione, Marcelo D Golemba, Carolina Torres, Maria Barrandeguy
Equine influenza virus (EIV) is considered the most important respiratory pathogen of horses as outbreaks of the disease lead to substantial economic losses. The H3N8 EIV has caused respiratory disease in horses across the world, including South American countries. Nucleotide and deduced amino acid sequences for the complete haemagglutinin gene of the H3N8 EIV detected in South America since 1963 were analyzed. Phylogenetic and Bayesian coalescent analyses were carried out to study the origin, the time of the most recent common ancestors (tMRCA), the demographic and the phylogeographic patterns of the H3N8 EIV...
October 16, 2016: Pathogens
Li Wei, Zhang Qiong, Shen Xiao-Ting, Liu Yu-Jie, Mao Jian-Hua, Shu Qiang, Shang Shi-Qiang
Enterovirus (EV) has over 100 serotypes of species A-D, which can cause various symptoms in infants. Enterovirus encephalitis (EVE) is serve disease with high morbidity and mortality in children. To well define the epidemiology of EVE, we wanted to know more about EV and EV molecular typing by conducting this study in Hangzhou.Cerebrospinal fluid samples were collected from children with diagnosis of encephalitis. Meanwhile, one-step real-time RT-PCR was used for the detection of EV, and we also identified the serotypes of EV by using gene sequencing of VP1 or 5'UTR region...
October 2016: Medicine (Baltimore)
Laura Pérez-Lago, Santiago Izco, Marta Herranz, Griselda Tudó, María Carcelén, Iñaki Comas, Olalla Sierra, Juliá González, María Jesús Ruiz-Serrano, Juan Eyene, Emilio Bouza, Darío García-de-Viedma
OBJECTIVE: Molecular epidemiology techniques in tuberculosis (TB) can identify high-risk strains that are actively transmitted. We aimed to implement a novel strategy to optimize the identification and control of MDR-TB in a specific population. METHODS: We developed a strain-specific-PCR tailored from whole-genome-sequencing (WGS) data to track a specific multidrug-resistant prevalent strain in Equatorial Guinea (EG-MDR). RESULTS: The PCR was applied prospectively on remnants of GeneXpert reaction mixtures owing to the lack of culture facilities in EG...
October 13, 2016: Clinical Microbiology and Infection
Thierry Kammalac Ngouana, Pascal Drakulovski, Donika Krasteva, Rufin Kuipou Toghueo, Charles Kouanfack, Jacques Reynes, Eric Delaporte, Fabrice Fekam Boyom, Michèle Mallié, Sébastien Bertout
The molecular epidemiology and the antifungal susceptibility profiles of Candida albicans are scarce in Cameroon. Authors studied the genetic diversity and the antifungal susceptibility of C. albicans isolates from Yaoundé HIV-infected patients. Clinical isolates were obtained by mycological diagnosis of oropharyngeal swabs, stools, urine, and vaginal swabs from patients. C. albicans isolates were confirmed by the Light cycler real-time PCR of the ITS1 region of the 5.8s ribosomal DNA. The ABC genotypes and the Hwp1 gene amplification were carried out with specific primers...
October 14, 2016: Medical Mycology: Official Publication of the International Society for Human and Animal Mycology
Yu-Chia Hsieh, Yu-Chun Lin, Yhu-Chering Huang
The purpose of this study is to evaluate the susceptibility trend of vancomycin, teicoplanin, daptomycin, and linezolid against methicillin-resistant Staphylococcus aureus (MRSA) blood isolates of different clones over an 11-year period.From 2000 to 2010, all bloodstream MRSA isolates from Chang Gung Memorial Hospital in Taiwan were prospectively collected. Three periods, namely 2000 to 2001, 2004 to 2005, and 2010, were included and 124 MRSA isolates were selected from each period. Minimum inhibitory concentrations (MICs) were determined by E-test...
October 2016: Medicine (Baltimore)
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