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Molecular-epidemiology

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https://www.readbyqxmd.com/read/28230168/phylogenetic-characterizations-of-highly-mutated-ev-b106-recombinants-showing-extensive-genetic-exchanges-with-other-ev-b-in-xinjiang-china
#1
Yang Song, Yong Zhang, Qin Fan, Hui Cui, Dongmei Yan, Shuangli Zhu, Haishu Tang, Qiang Sun, Dongyan Wang, Wenbo Xu
Human enterovirus B106 (EV-B106) is a new member of the enterovirus B species. To date, only three nucleotide sequences of EV-B106 have been published, and only one full-length genome sequence (the Yunnan strain 148/YN/CHN/12) is available in the GenBank database. In this study, we conducted phylogenetic characterisation of four EV-B106 strains isolated in Xinjiang, China. Pairwise comparisons of the nucleotide sequences and the deduced amino acid sequences revealed that the four Xinjiang EV-B106 strains had only 80...
February 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28225904/invasive-haemophilus-influenzae-disease-in-the-vaccine-era-in-rio-de-janeiro-brazil
#2
Mari Tuyama, Jessica Corrêa-Antônio, Jessica Schlackman, Jane W Marsh, Maria C Rebelo, Elaine O Cerqueira, Márcio Nehab, Fabíola Kegele, Getúlio F Carmo, Dominique Ca Thielmann, Paulo F Barroso, Lee H Harrison, David E Barroso
BACKGROUND: Haemophilus influenzae (Hi) serotype b (Hib) conjugate vaccine was incorporated into the infant immunisation schedule in Brazil in 1999, where Hib was one of the major etiologic sources of community-acquired bacterial meningitis. OBJECTIVES: The purpose of this study is to describe the molecular epidemiology of invasive Hi disease in Rio de Janeiro state, Brazil, before and after vaccine introduction. METHODS: Surveillance data from 1986 to 2014 were analysed...
March 2017: Memórias do Instituto Oswaldo Cruz
https://www.readbyqxmd.com/read/28225898/invasive-haemophilus-influenzae-disease-in-the-vaccine-era-in-rio-de-janeiro-brazil
#3
Mari Tuyama, Jessica Corrêa-Antônio, Jessica Schlackman, Jane W Marsh, Maria C Rebelo, Elaine O Cerqueira, Márcio Nehab, Fabíola Kegele, Getúlio F Carmo, Dominique Ca Thielmann, Paulo F Barroso, Lee H Harrison, David E Barroso
BACKGROUND: Haemophilus influenzae (Hi) serotype b (Hib) conjugate vaccine was incorporated into the infant immunisation schedule in Brazil in 1999, where Hib was one of the major etiologic sources of community-acquired bacterial meningitis. OBJECTIVES: The purpose of this study is to describe the molecular epidemiology of invasive Hi disease in Rio de Janeiro state, Brazil, before and after vaccine introduction. METHODS: Surveillance data from 1986 to 2014 were analysed...
February 16, 2017: Memórias do Instituto Oswaldo Cruz
https://www.readbyqxmd.com/read/28225788/molecular-detection-and-genotyping-of-enteroviruses-from-csf-samples-of-patients-with-suspected-sepsis-like-illness-and-or-aseptic-meningitis-from-2012-to-2015-in-west-bank-palestine
#4
Kamal Dumaidi, Amer Al-Jawabreh
BACKGROUND: Human enteroviruses (HEVs) are the most frequently reported cause of aseptic meningitis with or without CSF pleocytosis in childhood. Rapid detection and genotype of HEVs is essential to determine the causative agent and variant causing sepsis-like illness and/or aseptic meningitis. AIM: To investigate the molecular epidemiology of enteroviruses (EVs) among patients with sepsis-like illness and/or aseptic meningitis admitted to three major hospitals in West Bank, Palestine from 2012 to 2015...
2017: PloS One
https://www.readbyqxmd.com/read/28222757/spatiotemporal-dynamics-of-hiv-1-transmission-in-france-1999-2014-and-impact-of-targeted-prevention-strategies
#5
Antoine Chaillon, Asma Essat, Pierre Frange, Davey M Smith, Constance Delaugerre, Francis Barin, Jade Ghosn, Gilles Pialoux, Olivier Robineau, Christine Rouzioux, Cécile Goujard, Laurence Meyer, Marie-Laure Chaix
BACKGROUND: Characterizing HIV-1 transmission networks can be important in understanding the evolutionary patterns and geospatial spread of the epidemic. We reconstructed the broad molecular epidemiology of HIV from individuals with primary HIV-1 infection (PHI) enrolled in France in the ANRS PRIMO C06 cohort over 15 years. RESULTS: Sociodemographic, geographic, clinical, biological and pol sequence data from 1356 patients were collected between 1999 and 2014. Network analysis was performed to infer genetic relationships, i...
February 21, 2017: Retrovirology
https://www.readbyqxmd.com/read/28222189/molecular-epidemiology-of-mycobacterium-tuberculosis-complex-in-brussels-2010-2013
#6
Christelle Vluggen, Karine Soetaert, Guido Groenen, Maryse Wanlin, Martine Spitaels, Wouter Arrazola de Oñate, Maryse Fauville-Dufaux, Claude Saegerman, Vanessa Mathys
The tuberculosis (TB) incidence rate in Brussels-Capital Region is 3-fold higher than in Belgium as a whole. Eight years after the realization of initial prospective population-based molecular epidemiology investigations in this Region, a similar study over the period 2010-2013 was conducted. TB strains isolated from 945 patients were submitted to genotyping by standardized 24-locus-MIRU-VNTR typing and spoligotyping. The phylogenetic analysis showed that the LAM (16.7%) and Haarlem (15.7%) branches are the two most prevalent TB lineages circulating in Brussels...
2017: PloS One
https://www.readbyqxmd.com/read/28222182/epidemiological-tracing-of-bovine-tuberculosis-in-switzerland-multilocus-variable-number-of-tandem-repeat-analysis-of-mycobacterium-bovis-and-mycobacterium-caprae
#7
Giovanni Ghielmetti, Simone Scherrer, Ute Friedel, Daniel Frei, Dominique Suter, Lukas Perler, Max M Wittenbrink
BACKGROUND: After 15 years of absence, in 2013 bovine tuberculosis (bTB), caused by Mycobacterium (M.) bovis and M. caprae, reemerged in the Swiss dairy cattle population. In order to identify the sources of infection as well as the spread of the agents, molecular-epidemiologic tracing by MIRU-VNTR analysis in combination with spoligotyping was performed. A total of 17 M. bovis and 7 M. caprae isolates were cultured from tuberculous bovine lymph nodes and analyzed with a set of 49 genetic markers by using automated capillary electrophoresis...
2017: PloS One
https://www.readbyqxmd.com/read/28220547/identification-and-molecular-epidemiology-of-dermatophyte-isolates-by-repetitive-sequence-pcr-based-dna-fingerprinting-using-the-diversilab-system-in-turkey
#8
A Nedret Koc, Mustafa A Atalay, Melek Inci, Fatma M Sariguzel, Hafize Sav
Dermatophyte species, isolation and identification in clinical samples are still difficult and take a long time. The identification and molecular epidemiology of dermatophytes commonly isolated in a clinical laboratory in Turkey by repetitive sequence-based PCR (rep-PCR) were assessed by comparing the results with those of reference identification. A total of 44 dermatophytes isolated from various clinical specimens of 20 patients with superficial mycoses in Kayseri and 24 patients in Hatay were studied. The identification of dermatophyte isolates was based on the reference identification and rep-PCR using the DiversiLab System (BioMerieux)...
February 21, 2017: Mycoses
https://www.readbyqxmd.com/read/28220115/spread-of-the-blaoxa-23-containing-tn2008-in-carbapenem-resistant-acinetobacter-baumannii-isolates-grouped-in-cc92-from-china
#9
Yisheng Chen, Jing Gao, Haomin Zhang, Chunmei Ying
The rapid expansion of carbapenem-resistant Acinetobacter baumannii (CRAB) clinical isolates is a big issue. We investigated the antibiotic susceptibility, molecular epidemiology and resistance gene of A. baumannii collected at two hospitals in Shanghai, China. Besides, the A. baumannii PCR-based replicon typing method (AB-PBRT) was conducted to categorize the plasmids into homogeneous groups on the basis of replicase genes. Most CRAB isolates showed high-level resistance to almost all antibiotics but retain susceptibility to colistin and tigecycline...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28219746/application-of-high-throughput-sequencing-to-whole-rabies-viral-genome-characterisation-and-its-use-for-phylogenetic-re-evaluation-of-a-raccoon-strain-incursion-into-the-province-of-ontario
#10
Susan A Nadin-Davis, Adam Colville, Hannah Trewby, Roman Biek, Leslie Real
Raccoon rabies remains a serious public health problem throughout much of the eastern seaboard of North America due to the urban nature of the reservoir host and the many challenges inherent in multi-jurisdictional efforts to administer co-ordinated and comprehensive wildlife rabies control programmes. Better understanding of the mechanisms of spread of rabies virus can play a significant role in guiding such control efforts. To facilitate a detailed molecular epidemiological study of raccoon rabies virus movements across eastern North America, we developed a methodology to efficiently determine whole genome sequences of hundreds of viral samples...
February 17, 2017: Virus Research
https://www.readbyqxmd.com/read/28219668/outbreak-of-dengue-virus-type-3-in-malakand-pakistan-2015-a-laboratory-perspective
#11
Muhammad Suleman, Rani Faryal, Muhammad Masroor Alam, Adnan Khurshid, Salmaan Sharif, Shahzad Shaukat, Mehar Angez, Massab Umair, Mian Muhammad Sufian, Yasir Arshad, Tanveer Inam, Syed Sohail Zahoor Zaidi
An outbreak of dengue fever was reported in Malakand district, Khyber Pakhtunkhwa (KP) province of Pakistan during 2015. Detection of viral RNA by real-time PCR confirmed dengue virus serotype-3 (DENV-3) to be the causative agent causing the outbreak. Phylogenetic analysis based on partial E-NS1 gene sequences showed that the DENV-3 viruses belonged to genotype III with maximum homology with the dengue-3 strains previously reported from Pakistan and India. Our current report provides updated information on molecular epidemiology and phylogenetic analysis of dengue virus serotypes responsible for 2015 outbreak in KP...
February 17, 2017: Acta Tropica
https://www.readbyqxmd.com/read/28219454/the-characterization-of-bordetella-pertussis-strains-isolated-in-the-central-western-region-of-brazil-suggests-the-selection-of-a-specific-genetic-profile-during-2012-2014-outbreaks
#12
E L Rocha, D Leite, C H Camargo, L M Martins, R S N Silva, V P Martins, T A Campos
Pertussis is a worldwide acute respiratory disease caused by the bacterium Bordetella pertussis. Despite high vaccine coverage, the bacterium continues to circulate in populations and is still one of the most common vaccine-preventable diseases. In Brazil, pertussis incidence has presented a significant decrease since 1990 but since 2011 a sudden increase in incidence has been observed. Thus, the aim of this study was to perform a molecular epidemiological characterization of B. pertussis strains isolated in the Central-Western region (specifically in Distrito Federal) of Brazil from August 2012 to August 2014...
February 21, 2017: Epidemiology and Infection
https://www.readbyqxmd.com/read/28218261/pneumococcal-prophages-are-diverse-but-not-without-structure-or-history
#13
Angela B Brueggemann, Caroline L Harrold, Reza Rezaei Javan, Andries J van Tonder, Angus J McDonnell, Ben A Edwards
Bacteriophages (phages) infect many bacterial species, but little is known about the diversity of phages among the pneumococcus, a leading global pathogen. The objectives of this study were to determine the prevalence, diversity and molecular epidemiology of prophages (phage DNA integrated within the bacterial genome) among pneumococci isolated over the past 90 years. Nearly 500 pneumococcal genomes were investigated and RNA sequencing was used to explore prophage gene expression. We revealed that every pneumococcal genome contained prophage DNA...
February 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28217117/the-promise-of-whole-genome-pathogen-sequencing-for-the-molecular-epidemiology-of-emerging-aquaculture-pathogens
#14
REVIEW
Sion C Bayliss, David W Verner-Jeffreys, Kerry L Bartie, David M Aanensen, Samuel K Sheppard, Alexandra Adams, Edward J Feil
Aquaculture is the fastest growing food-producing sector, and the sustainability of this industry is critical both for global food security and economic welfare. The management of infectious disease represents a key challenge. Here, we discuss the opportunities afforded by whole genome sequencing of bacterial and viral pathogens of aquaculture to mitigate disease emergence and spread. We outline, by way of comparison, how sequencing technology is transforming the molecular epidemiology of pathogens of public health importance, emphasizing the importance of community-oriented databases and analysis tools...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28215875/occurrence-and-molecular-genotyping-of-giardia-duodenalis-and-cryptosporidium-spp-in-wild-mesocarnivores-in-spain
#15
Marta Mateo, Marta Hernández de Mingo, Aida de Lucio, Lucía Morales, Ana Balseiro, Alberto Espí, Marta Barral, José Francisco Lima Barbero, Miguel Ángel Habela, José L Fernández-García, Rafael Calero Bernal, Pamela C Köster, Guillermo A Cardona, David Carmena
There is a surprisingly scarce amount of epidemiological and molecular data on the prevalence, frequency, and diversity of the intestinal protozoan parasites Giardia duodenalis and Cryptosporidium spp. in wildlife in general and mesocarnivore species in particular. Consequently, the extent of the cyst/oocyst environmental contamination attributable to these wild host species and their potential implications for public veterinary health remain largely unknown. In this molecular epidemiological survey a total of 193 individual faecal samples from badgers (Meles meles, n=70), ferrets (Mustela putorius furo, n=2), genets (Genetta genetta, n=6), Iberian lynxes (Lynx pardinus, n=6), beech martens (Martes foina, n=8), mongooses (Herpestes ichneumon, n=2), otters (Lutra lutra, n=2), polecats (Mustela putorius, n=2), red foxes (Vulpes vulpes, n=87), wildcats (Felis silvestris, n=2), and wolves (Canis lupus, n=6) were obtained from road-killed, hunted, and accidentally found carcasses, and from camera-trap surveys or animals entering rescue shelters, during the period December 2003-April 2016...
February 15, 2017: Veterinary Parasitology
https://www.readbyqxmd.com/read/28213654/molecular-epidemiology-of-leptospira-serogroup-pomona-infections-among-wild-and-domestic-animals-in-spain
#16
Z J Arent, C Gilmore, J M San-Miguel Ayanz, L Quevedo Neyra, F J García-Peña
Strains of Leptospira serogroup Pomona are known to cause widespread animal infections in many parts of the world. Forty-three isolates retrieved from domestic animals and wild small mammals suggest that serogroup Pomona is epidemiologically relevant in Spain. This is supported by the high prevalence of serovar Pomona antibodies in livestock and wild animals. In this study, the strains were serologically and genetically characterized in an attempt to elucidate their epidemiology. Serological typing was based on the microscopic agglutination test but molecular typing involved species-specific polymerase chain reaction, restriction endonuclease analysis, and multiple-locus variable-number tandem repeat analysis...
February 17, 2017: EcoHealth
https://www.readbyqxmd.com/read/28213546/environmental-surveillance-of-norovirus-genogroups-i-and-ii-for-sensitive-detection-of-epidemic-variants
#17
Shinobu Kazama, Takayuki Miura, Yoshifumi Masago, Yoshimitsu Konta, Kentaro Tohma, Takafumi Manaka, Xiaofang Liu, Daisuke Nakayama, Takashi Tanno, Mayuko Saito, Hitoshi Oshitani, Tatsuo Omura
Sewage samples have been investigated to study the level of noroviruses concentration in sewage or the genotypes of noroviruses circulating in human populations. However, the statistical relationship between the concentration of the virus and the number of infected individuals, and the clinical importance of genotypes or strains detected in sewage are unclear. In this study, we carried out both environmental and clinical surveillance of noroviruses for three years: 2013-2016. We performed cross-correlation analysis between the concentrations of norovirus GI or GII in sewage samples collected weekly and the number of gastroenteritis cases...
February 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28212676/genetic-diversity-and-selection-of-three-nuclear-genes-in-schistosoma-japonicum-populations
#18
Yaqi Li, Mingbo Yin, Qunfeng Wu, Donald P McManus, David Blair, Hongyan Li, Bin Xu, Xiaojin Mo, Zheng Feng, Wei Hu
BACKGROUND: The blood fluke, Schistosoma japonicum still causes severe disease in China, the Philippines and Indonesia. Although there have been some studies the molecular epidemiology of this persistent and harmful parasite, few have explored the possibility and implications of selection in S. japonicum populations. METHODS: We analyzed diversity and looked for evidence of selection at three nuclear genes (SjIpp2, SjFabp and SjT22.6) in 13 S. japonicum populations...
February 17, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28208132/an-outbreak-of-acute-hepatitis-caused-by-genotype-ib-hepatitis-a-viruses-contaminating-the-water-supply-in-thailand
#19
Kriangsak Ruchusatsawat, Jongkonnee Wongpiyabovorn, Chonthicha Kawidam, Laddawan Thiemsing, Somchai Sangkitporn, Sayaka Yoshizaki, Masashi Tatsumi, Naokazu Takeda, Koji Ishii
BACKGROUND: In 2000, an outbreak of acute hepatitis A was reported in a province adjacent to Bangkok, Thailand. AIMS: To investigate the cause of the 2000 hepatitis A outbreaks in Thailand using molecular epidemiological analysis. METHODS: Serum and stool specimens were collected from patients who were clinically diagnosed with acute viral hepatitis. Water samples from drinking water and deep-drilled wells were also collected. These specimens were subjected to polymerase chain reaction (PCR) amplification and sequencing of the VP1/2A region of the hepatitis A virus (HAV) genome...
February 17, 2017: Intervirology
https://www.readbyqxmd.com/read/28202801/molecular-epidemiology-and-strain-comparison-between-hepatitis-e-virus-in-human-sera-and-pig-livers-during-2014-2016-in-hong-kong
#20
Martin C W Chan, Kirsty Kwok, Tin-Nok Hung, Paul K S Chan
Hepatitis E virus (HEV) causes substantial morbidity and mortality in developing countries and is considered an emerging food-borne pathogen in previously non-endemic developed countries. To investigate genetic association between human HEV infection and HEV-contaminated high-risk food in Hong Kong, we compared local virus strains obtained from hepatitis E patient sera with those surveyed from high-risk food items during 2014-2016. Twenty-four cases of laboratory-confirmed human HEV infections were identified from January 2014 to March 2016 in our hospitals...
February 15, 2017: Journal of Clinical Microbiology
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