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Molecular-epidemiology

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https://www.readbyqxmd.com/read/28926571/whole-genome-sequencing-illuminates-the-evolution-and-spread-of-multidrug-resistant-tuberculosis-in-southwest-nigeria
#1
Madikay Senghore, Jacob Otu, Adam Witney, Florian Gehre, Emma L Doughty, Gemma L Kay, Phillip Butcher, Kayode Salako, Aderemi Kehinde, Nneka Onyejepu, Emmanuel Idigbe, Tumani Corrah, Bouke de Jong, Mark J Pallen, Martin Antonio
Nigeria has an emerging problem with multidrug-resistant tuberculosis (MDR-TB). Whole-genome sequencing was used to understand the epidemiology of tuberculosis and genetics of multi-drug resistance among patients from two tertiary referral centers in Southwest Nigeria. In line with previous molecular epidemiology studies, most isolates of Mycobacterium tuberculosis from this dataset belonged to the Cameroon clade within the Euro-American lineage. Phylogenetic analysis showed this clade was undergoing clonal expansion in this region, and suggests that it was involved in community transmission of sensitive and multidrug-resistant tuberculosis...
2017: PloS One
https://www.readbyqxmd.com/read/28921008/molecular-characterization-of-very-virulent-infectious-bursal-disease-virus-strains-circulating-in-egypt-from-2003-to-2014
#2
Awad A Shehata, Hesham Sultan, Mohammed Y Halami, Shaimaa Talaat, Thomas W Vahlenkamp
In the present study, four very virulent infectious bursal disease virus (vvIBDV) isolates from flocks of chickens with vaccination failure in Egypt in 2003, 2007, 2010 and 2014 were characterized. The four viruses, designated USC2003, USC2007, USC2010 and USC2014, were detected by reverse transcription PCR, subjected to sequencing of both genomic segments (A and B) and compared with geographically and phylogenetically diverse IBDV strains. Phylogenetic analysis of segment A (complete) and B (partial) revealed a close relationship between Egyptian and vvIBDV reference strains of European and Asian origin...
September 18, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28919546/phylodynamics-of-the-brazilian-feline-immunodeficiency-virus
#3
Lucía Cano-Ortiz, Dennis Maletich Junqueira, Juliana Comerlato, Cristina Santos Costa, André Zani, Naila Blatt Duda, Caroline Tochetto, Raissa Nunes Dos Santos, Fernanda Vieira Amorim da Costa, Paulo Roehe, Ana Cláudia Franco
Feline immunodeficiency virus (FIV), like other retroviruses, displays large genomic divergence when different isolates are compared. In this study, 31 FIV positive samples of domestic cats from Porto Alegre, RS, Brazil were used aiming at a detailed genomic characterization and a better understanding of the molecular epidemiology of the virus in Brazil. The proviral env genes were partially amplified, sequenced and compared with another 237 sequences from different continents. We identified several Brazilian highly supported clades (A, B1, B2, C and D) that suggest independent events of introduction of FIV in Brazil...
September 12, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28918144/short-communication-molecular-epidemiology-of-streptococcus-agalactiae-differs-between-countries
#4
J Reyes, M Chaffer, Juan Carlos Rodriguez-Lecompte, Javier Sánchez, Ruth N Zadoks, Natasha Robinson, Ximena Cardona, N Ramírez, G P Keefe
Group B Streptococcus or Streptococcus agalactiae continue to be challenging for milk quality programs in countries with emerging dairy industries, such as Colombia, where high prevalence has been reported. Molecular typing of isolates is needed to understand the variability and epidemiology of this pathogen and to develop effective control and eradication programs. We characterized the molecular profile of Strep. agalactiae isolated from cows with subclinical mastitis in 21 Colombian dairy herds and measured diversity within and between herds using multilocus sequence typing...
September 13, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28915725/distribution-of-rotavirus-genotypes-ccirculating-in-ahvaz-iran-in-2016
#5
Azarakhsh Azaran, Manoochehr Makvandi, Ali Teimoori, Saeedeh Ebrahimi, Farzad Heydari, Roya Nikfar
Background: Group A rotavirus (RVA) mainly causes acute gastroenteritis, exclusively in young children in developing countries. The prevalence and determination of the molecular epidemiology of rotavirus genotypes will determine the dominant rotavirus genotypes in the region and provide a strategy for the development of appropriate vaccines. Methods: A total of 100 fecal samples were collected from children below five years with acute gastroenteritis who referred to Aboozar Children’s Hospital of Ahvaz city during October 2015 to March 2016...
September 16, 2017: Iranian Biomedical Journal
https://www.readbyqxmd.com/read/28912478/the-molecular-epidemiology-of-hiv-1-in-the-comunidad-valenciana-spain-analysis-of-transmission-clusters
#6
Juan Ángel Patiño-Galindo, Manoli Torres-Puente, María Alma Bracho, Ignacio Alastrué, Amparo Juan, David Navarro, María José Galindo, Dolores Ocete, Enrique Ortega, Concepción Gimeno, Josefina Belda, Victoria Domínguez, Rosario Moreno, Fernando González-Candelas
HIV infections are still a very serious concern for public heath worldwide. We have applied molecular evolution methods to study the HIV-1 epidemics in the Comunidad Valenciana (CV, Spain) from a public health surveillance perspective. For this, we analysed 1804 HIV-1 sequences comprising protease and reverse transcriptase (PR/RT) coding regions, sampled between 2004 and 2014. These sequences were subtyped and subjected to phylogenetic analyses in order to detect transmission clusters. In addition, univariate and multinomial comparisons were performed to detect epidemiological differences between HIV-1 subtypes, and risk groups...
September 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28911852/molecular-epidemiology-and-the-resistance-and-virulence-properties-of-pseudomonas-aeruginosa-cross-colonization-clonal-isolates-in-the-non-outbreak-setting
#7
Pengwei Hu, Jiayi Chen, Yuhang Chen, Tao Zhou, Xin Xu, Xiaofang Pei
The molecular epidemiology of Pseudomonas aeruginosa cross-colonization isolates has received limited attention in the non-outbreak setting. Also the roles of P. aeruginosa resistance and virulence in cross-colonization need to be further studied. This study aims to launch a tracking investigation to determine the epidemiological relationship of P. aeruginosa clinical and environmental isolates, identify the cross-colonization routes, and characterize the resistance and virulence properties of clonal clusters and sporadic strains in the respiratory care wards of a tertiary care hospital...
September 11, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28911835/molecular-characterisation-of-equine-group-a-rotaviruses-in-ireland-2011-2015
#8
Manabu Nemoto, Evelyn Ryan, Pamela Lyons, Ann Cullinane
The molecular epidemiology of equine group A rotaviruses (RVAs) in Ireland from 2011 to 2015 was investigated. Of 438 diagnostic specimens submitted from foals with enteric disease, 102 (23.3%) were positive for RVA using an immunochromatographic assay. G genotypes were determined for 76 equine RVAs, of which 68 (89.5%) were G3 and eight (10.5%) were G14. Of 18 RVAs (12 G3 and six G14) characterised by P genotyping, all were P[12]. G3P[12] and G14P[12] were the most prevalent genotypes of RVA in foals in Ireland, similar to other countries and consistent with previous studies in Ireland from 1999 to 2005...
August 2017: Veterinary Journal
https://www.readbyqxmd.com/read/28906005/group-a-rotaviruses-circulating-prior-to-a-national-immunization-programme-in-nigeria-clinical-manifestations-high-g12p-8-frequency-intra-genotypic-divergence-of-vp4-and-vp7
#9
M O Japhet, O Famurewa, M Iturriza-Gomara, O A Adesina, O O Opaleye, S Niendorf, C T Bock, A Mas Marques
Nigeria having approximately 50,000 Rotavirus A (RVA) deaths annually is yet to introduce RVA vaccine into routine national immunization; therefore surveillance of RVA strains circulating before vaccine introduction is essential in evaluating impact of the intervention. Stool samples and sociodemographic data of diarrhoeic children, <5 years were collected between August 2012 and December 2013. While a high prevalence of RVA infection (47.6%; 49/103) was observed by quantitative reverse transcription real time PCR, only 25% (26/103) had high RVA genome concentrations and were antigen positive...
September 14, 2017: Journal of Medical Virology
https://www.readbyqxmd.com/read/28904978/corrigendum-to-molecular-epidemiological-investigation-of-porcine-kobuvirus-and-its-coinfection-rate-with-pedv-and-sav-in-northwest-china
#10
Chen Wang, Xi Lan, Bin Yang
[This corrects the article DOI: 10.1155/2016/7590569.].
2017: BioMed Research International
https://www.readbyqxmd.com/read/28902922/molecular-clustering-of-patients-with-diabetes-and-pulmonary-tuberculosis-a-systematic-review-and-meta-analysis
#11
Francles Blanco-Guillot, Guadalupe Delgado-Sánchez, Norma Mongua-Rodríguez, Pablo Cruz-Hervert, Leticia Ferreyra-Reyes, Elizabeth Ferreira-Guerrero, Mercedes Yanes-Lane, Rogelio Montero-Campos, Miriam Bobadilla-Del-Valle, Pedro Torres-González, Alfredo Ponce-de-León, José Sifuentes-Osornio, Lourdes Garcia-Garcia
INTRODUCTION: Many studies have explored the relationship between diabetes mellitus (DM) and tuberculosis (TB) demonstrating increased risk of TB among patients with DM and poor prognosis of patients suffering from the association of DM/TB. Owing to a paucity of studies addressing this question, it remains unclear whether patients with DM and TB are more likely than TB patients without DM to be grouped into molecular clusters defined according to the genotype of the infecting Mycobacterium tuberculosis bacillus...
2017: PloS One
https://www.readbyqxmd.com/read/28902847/first-insights-in-the-variability-of-borrelia-recurrentis-genomes
#12
Durdica Marosevic, Gabriele Margos, Reinhard Wallich, Andreas Wieser, Andreas Sing, Volker Fingerle
BACKGROUND: Borrelia recurrentis is the causative agent of louse-borne relapsing fever, endemic to the Horn of Africa. New attention was raised in Europe, with the highest number of cases (n = 45) reported among migrants in 2015 in Germany and sporadically from other European countries. So far only one genome was sequenced, hindering the development of specific molecular diagnostic and typing tools. Here we report on modified culture conditions for B. recurrentis and the intraspecies genome variability of six isolates isolated and cultured in different years in order to explore the possibility to identify new targets for typing and examine the molecular epidemiology of the pathogen...
September 13, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28899610/nosocomial-acquired-and-community-onset-clostridium-difficile-infection-at-an-academic-hospital-in-italy-epidemiology-recurrences-and-toxin-genes-distribution
#13
Valeria Visconti, Grazia Brunetti, Maria Rosaria Cuomo, Alessandra Giordano, Giammarco Raponi
Toxinogenic Clostridium difficile infection (CDI) is a leading cause of infectious diarrhea. In this retrospective cohort study the molecular epidemiology of hospital-acquired and community-associated CDI was investigated in patients admitted to a tertiary care hospital. CD in stools samples was revealed by a two steps diagnostic algorithm, firstly screening for positivity to GDH antigen and thereafter RT-PCR analysis. Increased CDI incidence was observed ranging from 1.70episodes/10000patient-days in the 1st year, to 2...
September 9, 2017: Journal of Infection and Chemotherapy: Official Journal of the Japan Society of Chemotherapy
https://www.readbyqxmd.com/read/28893615/molecular-epidemiology-and-environmental-contamination-during-an-outbreak-of-parainfluenza-virus-3-in-a-hematology-ward
#14
Taeeun Kim, Choong Eun Jin, Heungsup Sung, Bonhan Koo, Joungha Park, Sun-Mi Kim, Ji Yeun Kim, Yong Pil Chong, Sang-Oh Lee, Sang-Ho Choi, Yang Soo Kim, Jun Hee Woo, Jung-Hee Lee, Je-Hwan Lee, Kyoo-Hyung Lee, Yong Shin, Sung-Han Kim
BACKGROUND: Although fomites or contaminated surfaces have been considered as transmission routes, the role of environmental contamination by human parainfluenza virus type 3 (hPIV-3) in healthcare settings is not established. AIM: To describe an hPIV-3 nosocomial outbreak and the results of environmental sampling to elucidate the source of nosocomial transmission and the role of environmental contamination. METHODS: During an hPIV-3 outbreak between May and June 2016, we swabbed environmental surfaces in contact with clustered patients and used respiratory specimens from infected patients and epidemiologically unlinked controls...
September 8, 2017: Journal of Hospital Infection
https://www.readbyqxmd.com/read/28891459/prevalence-of-clostridium-difficile-infection-and-colonization-in-a-tertiary-hospital-and-elderly-community-of-north-eastern-peninsular-malaysia
#15
N H Zainul, Z F Ma, A Besari, H Siti Asma, R A Rahman, D A Collins, N Hamid, T V Riley, Y Y Lee
Little is known about Clostridium difficile infection (CDI) in Asia. The aims of our study were to explore (i) the prevalence, risk factors and molecular epidemiology of CDI and colonization in a tertiary academic hospital in North-Eastern Peninsular Malaysia; (ii) the rate of carriage of C. difficile among the elderly in the region; (iii) the awareness level of this infection among the hospital staffs and students. For stool samples collected from hospital inpatients with diarrhea (n = 76) and healthy community members (n = 138), C...
September 11, 2017: Epidemiology and Infection
https://www.readbyqxmd.com/read/28888632/genotypic-and-geographical-distribution-of-porcine-reproductive-and-respiratory-syndrome-viruses-in-mainland-china-in-1996-2016
#16
Jia-Cong Gao, Jun-Yao Xiong, Chao Ye, Xiao-Bo Chang, Jin-Chao Guo, Cheng-Gang Jiang, Gui-Hong Zhang, Zhi-Jun Tian, Xue-Hui Cai, Guang-Zhi Tong, Tong-Qing An
Porcine reproductive and respiratory syndrome (PRRS) has caused huge economic losses to Chinese swine industry and remains a major threat since it was first reported in 1996. However, investigations of molecular epidemiological and genetic diversity of PRRS viruses (PRRSVs) in China were limited to a small number of representative strains collected in several areas. Moreover, lineage classifications reported by individual researchers were quite different. In the present study, we sequenced ORF5 sequences of 217 PRRSVs from clinical samples, retrieved all the available ORF5 sequences of PRRSVs isolated in China in 1996-2016 (n=2213) from GenBank, and systematically analyzed corresponding epidemiological data...
September 2017: Veterinary Microbiology
https://www.readbyqxmd.com/read/28887291/molecular-epidemiology-and-antimicrobial-susceptibility-of-methicillin-resistant-staphylococcus-aureus-isolates-in-xiangyang-china
#17
Yi-Tong Tang, Rui Cao, Na Xiao, Zhi-Shan Li, Rong Wang, Jiu-Ming Zou, Jiao Pei
OBJECTIVES: Methicillin-resistant Staphylococcus aureus (MRSA) is a public health problem worldwide. This study aimed to investigate the antimicrobial susceptibilities and molecular epidemiological characteristics of MRSA strains in Xiangyang, China, during 2012-2014. METHODS: Eighty non-duplicate S. aureus isolates from clinical specimens were collected from four tertiary hospitals. MRSA strains were identified and tested for antibacterial susceptibility. Staphylococcus cassette chromosome mec (SCCmec) typing, Pulsed-field gel electrophoresis (PFGE), multi-locus sequence typing (MLST) and spa typing were performed to explore molecular characteristics...
September 5, 2017: Journal of Global Antimicrobial Resistance
https://www.readbyqxmd.com/read/28887101/molecular-epidemiological-haematological-and-biochemical-evaluation-in-asymptomatic-theileria-annulata-infected-cattle-from-an-endemic-region-in-spain
#18
Lydia Calleja-Bueno, Ángel Sainz, Mercedes García-Sancho, Fernando Rodríguez-Franco, Juan V González-Martín, Alejandra Villaescusa
Mediterranean theileriosis is one of the most fatal theilerioses, with considerable economic impact on livestock production. The potential consequences of asymptomatic infection on the animal's health and on the epidemiology in endemic regions are still unclear. The objectives of this study were to determine the molecular prevalence of T. annulata in a representative population of asymptomatic cattle in extensive management in Madrid, Central Spain, an area where practitioners frequently report cases of clinical theileriosis, and to evaluate the existence of associations between infection by this pathogen and haematological, biochemical and epidemiological data...
August 25, 2017: Ticks and Tick-borne Diseases
https://www.readbyqxmd.com/read/28880958/think-globally-act-locally-phylodynamic-reconstruction-of-infectious-bronchitis-virus-ibv-qx-genotype-gi-19-lineage-reveals-different-population-dynamics-and-spreading-patterns-when-evaluated-on-different-epidemiological-scales
#19
Giovanni Franzo, Paola Massi, Claudia Maria Tucciarone, Ilaria Barbieri, Giovanni Tosi, Laura Fiorentini, Massimo Ciccozzi, Antonio Lavazza, Mattia Cecchinato, Ana Moreno
Infectious bronchitis virus (IBV) represents one of the poultry industry major threats, particularly in high density producing countries. The emergence and spread of new IBV genotypes have frustrated the various disease control efforts implemented over time. Despite that, few comprehensive and large scale studies have been performed to understand the international and local spreading dynamics of this virus. In the present work, these phenomena were evaluated by implementing a Bayesian phylodynamic approach to reconstruct the epidemiological patterns and population history of the QX genotype (currently renamed GI-19 lineage), the most relevant IBV lineage of the Old-World...
2017: PloS One
https://www.readbyqxmd.com/read/28880944/spatiotemporal-and-molecular-epidemiology-of-cutaneous-leishmaniasis-in-libya
#20
Ahmad Amro, Hamida Al-Dwibe, Aisha Gashout, Olga Moskalenko, Marlena Galafin, Omar Hamarsheh, Marcus Frohme, Anja Jaeschke, Gabriele Schönian, Katrin Kuhls
BACKGROUND: Cutaneous leishmaniasis (CL) is a major public health problem in Libya. In this paper, we describe the eco-epidemiological parameters of CL during the armed conflict period from January 2011 till December 2012. Current spatiotemporal distributions of CL cases were explored and projected to the future using a correlative modelling approach. In addition the present results were compared with our previous data obtained for the time period 1995-2008. METHODOLOGY/PRINCIPAL FINDINGS: We investigated 312 CL patients who presented to the Dermatology Department at the Tripoli Central Hospital and came from 81 endemic areas distributed in 10 districts...
September 7, 2017: PLoS Neglected Tropical Diseases
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