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Molecular-epidemiology

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https://www.readbyqxmd.com/read/28107671/recent-sequence-variation-in-probe-binding-site-affected-detection-of-respiratory-syncytial-virus-group-b-by-real-time-rt-pcr
#1
Everlyn Kamau, Charles N Agoti, Clement S Lewa, John Oketch, Betty E Owor, Grieven P Otieno, Anne Bett, Patricia A Cane, D James Nokes
BACKGROUND: Direct immuno-fluorescence test (IFAT) and multiplex real-time RT-PCR have been central to RSV diagnosis in Kilifi, Kenya. Recently, these two methods showed discrepancies with an increasing number of PCR undetectable RSV-B viruses. OBJECTIVES: Establish if mismatches in the primer and probe binding sites could have reduced real-time RT-PCR sensitivity. STUDY DESIGN: Nucleoprotein (N) and glycoprotein (G) genes were sequenced for real-time RT-PCR positive and negative samples...
January 5, 2017: Journal of Clinical Virology: the Official Publication of the Pan American Society for Clinical Virology
https://www.readbyqxmd.com/read/28104383/virulence-traits-and-pathogenicity-of-uropathogenic-escherichia-coli-isolates-with-common-and-uncommon-o-serotypes
#2
Qingqing Gao, Debao Zhang, Zhengqin Ye, Xiaoping Zhu, Weixia Yang, Lanmei Dong, Song Gao, Xiufan Liu
Urinary tract infections (UTIs) are among the most common human diseases worldwide. This study aimed to collect uropathogenic Escherichia coli (UPEC) isolates from Jiangsu Province and obtain insights into the molecular epidemiology of UPEC in this region. The O serotypes, phylogenetic groups, and virulence factors of 183 UPEC isolates were determined. In this study, we isolated 51 UPEC isolates with common O serotypes including O1, O2, O4, O6, O7, O16, O18 and O75, as well as 35 of those with uncommonly encountered O serotypes including O8, O12, O15, O26, and O74...
January 16, 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/28100596/genomic-epidemiology-of-penicillin-non-susceptible-pneumococci-with-non-vaccine-serotypes-causing-invasive-disease-in-the-usa
#3
Cheryl P Andam, Patrick K Mitchell, Alanna Callendrello, Qiuzhi Chang, Jukka Corander, Chrispin Chaguza, Lesley McGee, Bernard W Beall, William P Hanage
Conjugate vaccination against seven pneumococcal serotypes (PCV7) reduced disease prevalence due to antibiotic resistant strains throughout the 2000s; however, disease caused by resistant non-vaccine type (NVT) strains increased. Some of these emerging strains were derived from vaccine types (VT) that had changed their capsule by recombination. The introduction of vaccine targeting 13 serotypes (PCV13) in 2010 has led to concern that this scenario will repeat itself. We generated high quality draft genomes from 265 isolates of NVT pneumococci not susceptible to penicillin (PNSP) in 2009 and compared them with 581 isolates from 2012-2013, collected by the Active Bacterial Core surveillance (ABCs) of the Centers for Disease Control and Prevention (CDC)...
January 18, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28100285/characterization-of-the-complete-mitochondrial-genome-of-setaria-digitata-nematoda-setariidae-from-china
#4
G-H Liu, J-Y Li, X-Q Zhu
Setaria digitata is a filarial parasite that causes fatal cerebrospinal nematodiasis in goats, horses and sheep, resulting in substantial economic losses to livestock farmers. In the present study, the complete mitochondrial (mt) genome of S. digitata from China was determined, characterized and compared with that of S. digitata from Sri Lanka. The identity of the mt genomes was 98.3% between S. digitata from China and Sri Lanka, and the complete mt genome sequence of S. digitata from China was slightly shorter (25 bp) than that from Sri Lanka...
January 19, 2017: Journal of Helminthology
https://www.readbyqxmd.com/read/28098174/novel-g9-rotavirus-strains-co-circulate-in-children-and-pigs-taiwan
#5
Fang-Tzy Wu, Krisztián Bányai, Baoming Jiang, Luke Tzu-Chi Liu, Szilvia Marton, Yhu-Chering Huang, Li-Min Huang, Ming-Hui Liao, Chao A Hsiung
Molecular epidemiologic studies collecting information of the spatiotemporal distribution of rotavirus VP7 (G) and VP4 (P) genotypes have shown evidence for the increasing global importance of genotype G9 rotaviruses in humans and pigs. Sequence comparison of the VP7 gene of G9 strains identified different lineages to prevail in the respective host species although some of these lineages appear to be shared among heterologous hosts providing evidence of interspecies transmission events. The majority of these events indicates the pig-to-human spillover, although a reverse route of transmission cannot be excluded either...
January 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28096619/detection-identification-and-differentiation-of-sheep-pox-virus-and-goat-pox-virus-from-clinical-cases-in-giza-governorate-egypt
#6
M A Mahmoud, M H Khafagi
AIM: To isolate, identify, and differentiate Capripoxviruses (CaPV) (sheep pox virus and goat pox virus) infections by egg inoculation, transmission electron microscopy (TEM), and 30 kDa RNA polymerase subunit gene-based polymerase chain reaction (PCR) (RPO30) in clinically affected animals in Hawamdia township of Giza Governorate, Egypt. MATERIALS AND METHODS: A total of 37 scab samples were collected from clinically suspected field cases of sheep pox and goat pox...
December 2016: Veterinary World
https://www.readbyqxmd.com/read/28095455/novel-porcine-epidemic-diarrhea-virus-pedv-variants-with-large-deletions-in-the-spike-s-gene-coexist-with-pedv-strains-possessing-an-intact-s-gene-in-domestic-pigs-in-japan-a-new-disease-situation
#7
Nguyen Van Diep, Junzo Norimine, Masuo Sueyoshi, Nguyen Thi Lan, Ryoji Yamaguchi
Since late 2013, after an absence of seven years, outbreaks of porcine epidemic diarrhea virus (PEDV) infection have reemerged and swept rapidly across Japan, resulting in significant economic losses. In this study, we report the emergence, mixed infection, and genetic characterization of 15 novel field PEDV variants with large genomic deletions. The sizes of deletion varied between 582 nt (194 aa) and 648 nt (216 aa) at positions 28-714 (10-238) on the S gene (protein). Among 17 PEDV samples isolated from individual pigs, all of them contained at least two distinct genotypes with large genomic deletions, and 94...
2017: PloS One
https://www.readbyqxmd.com/read/28093076/genetic-source-tracking-of-an-anthrax-outbreak-in-shaanxi-province-china
#8
Dong-Li Liu, Jian-Chun Wei, Qiu-Lan Chen, Xue-Jun Guo, En-Min Zhang, Li He, Xu-Dong Liang, Guo-Zhu Ma, Ti-Cao Zhou, Wen-Wu Yin, Wei Liu, Kai Liu, Yi Shi, Jian-Jun Ji, Hui-Juan Zhang, Lin Ma, Fa-Xin Zhang, Zhi-Kai Zhang, Hang Zhou, Hong-Jie Yu, Biao Kan, Jian-Guo Xu, Feng Liu, Wei Li
BACKGROUND: Anthrax is an acute zoonotic infectious disease caused by the bacterium known as Bacillus anthracis. From 26 July to 8 August 2015, an outbreak with 20 suspected cutaneous anthrax cases was reported in Ganquan County, Shaanxi province in China. The genetic source tracking analysis of the anthrax outbreak was performed by molecular epidemiological methods in this study. METHODS: Three molecular typing methods, namely canonical single nucleotide polymorphisms (canSNP), multiple-locus variable-number tandem repeat analysis (MLVA), and single nucleotide repeat (SNR) analysis, were used to investigate the possible source of transmission and identify the genetic relationship among the strains isolated from human cases and diseased animals during the outbreak...
January 17, 2017: Infectious Diseases of Poverty
https://www.readbyqxmd.com/read/28092604/replication-kinetics-of-neuropathogenic-and-non-neuropathogenic-equine-herpesvirus-type-1-ehv-1-strains-in-primary-murine-neurons-and-ed-cell-line
#9
J Cymerys, A Słońska, J Brzezicka, A Tucholska, A Chmielewska, J Rola, P Malik, M W Bańbura
Equine herpesvirus type 1 (EHV-1) causes respiratory infections, abortion and neurological disorders in horses. Molecular epidemiology studies have demonstrated that a single-point mutation in DNA polymerase gene, resulting in an amino acid variation (N752/D752), is significantly associated with the neuropathogenic potential of EHV-1 strains. The aim of the study was to elucidate if there are any differences between neuropathogenic (EHV-1 26) and non-neuropathogenic (Jan-E and Rac-H) EHV-1 strains in their ability to infect neuronal cells...
December 1, 2016: Polish Journal of Veterinary Sciences
https://www.readbyqxmd.com/read/28091338/molecular-epidemiological-analysis-to-assess-the-influence-of-pet-ownership-in-the-biodiversity-of-staphylococcus-aureus-and-mrsa-in-dog-and-non-dog-owning-healthy-households
#10
J C VAN Balen, T Landers, E Nutt, A Dent, A E Hoet
It has been suggested that zoonotic transmission of Staphylococcus aureus (SA) and methicillin-resistant S. aureus (MRSA) can occur between owners and their pets within the same household. However, the influence that pet-ownership could have in the biodiversity of SA/MRSA strains circulating among owners is not fully understood. The objective of this study was to perform a molecular epidemiological analysis to evaluate and compare the biodiversity of SA/MRSA strains in dog-owning and non-dog-owning healthy households within the same community...
January 16, 2017: Epidemiology and Infection
https://www.readbyqxmd.com/read/28090077/clinical-and-biological-insights-from-viral-genome-sequencing
#11
Charlotte J Houldcroft, Mathew A Beale, Judith Breuer
Whole-genome sequencing (WGS) of pathogens is becoming increasingly important not only for basic research but also for clinical science and practice. In virology, WGS is important for the development of novel treatments and vaccines, and for increasing the power of molecular epidemiology and evolutionary genomics. In this Opinion article, we suggest that WGS of viruses in a clinical setting will become increasingly important for patient care. We give an overview of different WGS methods that are used in virology and summarize their advantages and disadvantages...
January 16, 2017: Nature Reviews. Microbiology
https://www.readbyqxmd.com/read/28087306/molecular-epidemiological-analysis-of-human-and-chicken-derived-isolates-of-campylobacter-jejuni-in-japan-using-next-generation-sequencing
#12
Takayuki Ohishi, Kotaro Aoki, Yoshikazu Ishii, Masaru Usui, Yutaka Tamura, Michiko Kawanishi, Ohnishi Kenji, Kazuhiro Tateda
In this research, we analyzed the main sequence types (ST) and ST complexes of human- and chicken-derived isolates of Campylobacter jejuni in Japan by using multilocus sequence typing (MLST). We also analyzed lipooligosaccharide biosynthesis locus classes (LOS locus classes) and the numbers of isolates carrying genes coding resistance factors against various antibiotics, and observed their relationships. ST-21 complex was the main ST complex in isolates from humans (n = 38) and chickens (n = 25). None of the isolates showed resistance to imipenem, chloramphenicol, or erythromycin...
January 10, 2017: Journal of Infection and Chemotherapy: Official Journal of the Japan Society of Chemotherapy
https://www.readbyqxmd.com/read/28077590/molecular-epidemiology-of-ascaris-infection-among-pigs-in-iowa
#13
Jeba Jesudoss Chelladurai, Kaitlyn Murphy, Tymbrie Snobl, Christopher Bader, Cody West, Kylie Thompson, Matthew T Brewer
Ascaris is a large roundworm parasite that infects humans and pigs throughout the world. Molecular markers have been used to study parasite transmission in Ascaris-endemic and -nonendemic regions of the world. In the United States, ascariasis still persists in commercial swine and has been designated a neglected disease of poverty in humans. However, relatively few data are available for evaluation of zoonotic transmission. In the present study, we obtained adult worms from abattoirs and characterized each worm on the basis of the gene encoding nuclear internal transcribed sequence (ITS) and mitochondrial cox1 Restriction fragment-length polymorphism analysis of ITS revealed swine, human, and hybrid genotypes...
January 1, 2017: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/28072891/molecular-epidemiology-and-resistome-analysis-of-multidrug-resistant-st11-klebsiella-pneumoniae-strain-containing-multiple-copies-of-extended-spectrum-%C3%AE-lactamase-genes-using-whole-genome-sequencing
#14
Roshan DSouza, Naina Adren Pinto, Insik Hwang, Hwang Younjee, YoungLag Cho, Hyunsoo Kim, Dongeun Yong, Jongrak Choi, Kyungwon Lee, Yunsop Chong
The aim of this work was to investigate the mechanism responsible for multidrug resistance in ST11 Klebsiella pneumoniae YMC 2013/7/B3993 containing multiple copies of ESBL genes using multiple parallel sequencing technology. In-depth analysis of the strain revealed multiple copies of ESBL genes, 2 copies of blaSHV-12 and 1 copy of blaCTX-M-15. Furthermore, 1 copy of blaOXA-9 and 3 copies of blaTEM-1 were found. The insertion of Tn1331 was detected, which consisted of blaOXA-9, blaTEM-1, aac(6')-lb-cr, and aadA1 genes...
January 10, 2017: New Microbiologica
https://www.readbyqxmd.com/read/28071193/screening-of-esbl-producing-enterobacteriacae-concomitant-with-low-degree-of-transmission-in-intensive-care-and-bone-marrow-transplant-units
#15
Giuseppe Valenza, Monika Schulze, Petra Friedrich, Wulf Schneider-Brachert, Thomas Holzmann, Silke Nickel, Verena Lehner-Reindl, Christiane Höller
BACKGROUND: Extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-E) are spreading worldwide in both hospital and community settings. In this study, the molecular epidemiology and the transmission modalities of ESBL-E in intensive care- and bone marrow transplant were investigated. METHODS: All patients included in this study were screened for presence of ESBL-E on admission and weekly. Relevant β-lactamase genes were identified by PCR and sequencing...
January 10, 2017: Infectious Diseases
https://www.readbyqxmd.com/read/28070005/higher-complexity-of-infection-and-genetic-diversity-of-plasmodium-vivax-than-plasmodium-falciparum-across-all-malaria-transmission-zones-of-papua-new-guinea
#16
Abebe A Fola, G L Abby Harrison, Mita Hapsari Hazairin, Céline Barnadas, Manuel W Hetzel, Jonah Iga, Peter M Siba, Ivo Mueller, Alyssa E Barry
Plasmodium falciparum and Plasmodium vivax have varying transmission dynamics that are informed by molecular epidemiology. This study aimed to determine the complexity of infection and genetic diversity of P. vivax and P. falciparum throughout Papua New Guinea (PNG) to evaluate transmission dynamics across the country. In 2008-2009, a nationwide malaria indicator survey collected 8,936 samples from all 16 endemic provinces of PNG. Of these, 892 positive P. vivax samples were genotyped at PvMS16 and PvmspF3, and 758 positive P...
January 9, 2017: American Journal of Tropical Medicine and Hygiene
https://www.readbyqxmd.com/read/28069653/the-molecular-epidemiology-of-pf-k13-mutations-in-senegal-using-targeted-amplicon-deep-sequencing
#17
Eldin Talundzic, Yaye D Ndiaye, Awa B Deme, Christian Olsen, Dhruviben S Patel, Shweta Biliya, Rachel Daniels, Fredrik O Vannberg, Sarah K Volkman, Venkatachalam Udhayakumar, Daouda Ndiaye
The emergence of Plasmodium falciparum (Pf) resistance to artemisinin in Southeast Asia threatens malaria control and elimination activities worldwide. Multiple polymorphisms in the Pf kelch gene found in chromosome 13 (Pfk13) have been associated with artemisinin resistance. Surveillance of potential drug resistance loci within a population that may emerge under increasing drug pressure is an important public health activity. In this context, P. falciparum infections from an observational surveillance study in Senegal were genotyped using targeted amplicon deep sequencing (TADS) for Pfk13 polymorphisms...
January 9, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28069071/sporadic-cases-of-adult-measles-a-research-article
#18
Ranjan Premaratna, Nathasha Luke, Harsha Perera, Mahesh Gunathilake, Pubudu Amarasena, T G A Nilmini Chandrasena
BACKGROUND: Measles caused by a paramyxovirus, characterized by fever, malaise, cough, coryza conjunctivitis, a maculopapular rash is known to result in pneumonia, encephalitis and death. Fatal cases of measles in Sri Lanka are rare after implementation of the National Immunization Programme in 1984. Thereafter 0.1% case fatality rate was observed during October 1999-June 2000 which is a very low figure compared to other regional countries. Immunization guidelines were further revised in 2001, 2011 and in 2012 when additional immunization was recommended to age group 4-21 years; who are likely to have inadequate immunization, in order to achieve elimination of Measles by 2020...
January 10, 2017: BMC Research Notes
https://www.readbyqxmd.com/read/28068335/dengue-in-latin-america-systematic-review-of-molecular-epidemiological-trends
#19
José Ramos-Castañeda, Flavia Barreto Dos Santos, Ruth Martínez-Vega, Josélio Maria Galvão de Araujo, Graham Joint, Elsa Sarti
Dengue, the predominant arthropod-borne viral disease affecting humans, is caused by one of four distinct serotypes (DENV-1, -2, -3 or -4). A literature analysis and review was undertaken to describe the molecular epidemiological trends in dengue disease and the knowledge generated in specific molecular topics in Latin America, including the Caribbean islands, from 2000 to 2013 in the context of regional trends in order to identify gaps in molecular epidemiological knowledge and future research needs. Searches of literature published between 1 January 2000 and 30 November 2013 were conducted using specific search strategies for each electronic database that was reviewed...
January 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28065889/antimicrobial-resistance-in-staphylococcus-pseudintermedius-and-the-molecular-epidemiology-of-methicillin-resistant-s-pseudintermedius-in-small-animals-in-finland
#20
Thomas Grönthal, Marjut Eklund, Katariina Thomson, Heli Piiparinen, Tarja Sironen, Merja Rantala
OBJECTIVES: To investigate antimicrobial susceptibility in Staphylococcus pseudintermedius and the occurrence of methicillin-resistant S. pseudintermedius (MRSP), to explore the molecular structure of the MRSP population and to analyse risk factors for MRSP. METHODS: Susceptibility data for clinical S. pseudintermedius isolates in 2011-15 were analysed using WHONET. All MRSP isolates in 2010-14 (n = 362) were typed using PFGE. Representative isolates (n = 87) of clusters were analysed using MLST and staphylococcal cassette chromosome mec (SCCmec) typing...
January 8, 2017: Journal of Antimicrobial Chemotherapy
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