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Molecular-epidemiology

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https://www.readbyqxmd.com/read/28542162/carbapenem-resistant-klebsiella-pneumoniae-in-barbados-driving-change-in-practice-at-the-national-level
#1
Corey Forde, Bryan Stierman, Pilar Ramon-Pardo, Thais Dos Santos, Nalini Singh
INTRODUCTION: Carbapenem-resistant Klebsiella pneumoniae (CRKP) is of growing concern globally. The risk for transmission of antimicrobial resistant organisms across several continents to the Caribbean is a real one given its tourism industry. After a cluster of cases of CRKP were detected, several studies detailed in this report were initiated to better characterize the problem. METHODS: A hospital-wide point prevalence study and active surveillance were performed at Queen Elizabeth Hospital (QEH) in Barbados in 2013 to assess the prevalence of CRKP infection/colonization...
2017: PloS One
https://www.readbyqxmd.com/read/28540766/hiv-1-full-genome-phylogenetics-of-generalized-epidemics-in-sub-saharan-africa-impact-of-missing-nucleotide-characters-in-next-generation-sequences
#2
Oliver Ratmann, Chris Wymant, Caroline Colijn, Siva Danaviah, M Essex, Simon D W Frost, Astrid Gall, Simani Gaiseitsiwe, Mary Grabowski, Ronald Gray, Stephane Guindon, Arndt von Haeseler, Pontiano Kaleebu, Michelle Kendall, Alexey Kozlov, Justen Manasa, Bui Quang Minh, Sikhulile Moyo, Vladimir Novitsky, Rebecca Nsubuga, Sureshnee Pillay, Thomas C Quinn, David Serwadda, Deogratius Ssemwanga, Alexandros Stamatakis, Jana Trifinopoulos, Maria Wawer, Andrew Leigh Brown, Tulio de Oliveira, Paul Kellam, Deenan Pillay, Christophe Fraser
To characterize HIV-1 transmission dynamics in regions where the burden of HIV-1 is greatest, the 'Phylogenetics and Networks for Generalised HIV Epidemics in Africa' consortium (PANGEA-HIV) is sequencing full-genome viral isolates from across sub-Saharan Africa. We report the first 3,985 PANGEA-HIV consensus sequences from four cohort sites (Rakai Community Cohort Study, n=2,833; MRC/UVRI Uganda, n=701; Mochudi Prevention Project, n=359; Africa Health Research Institute Resistance Cohort, n=92). Next-generation sequencing success rates varied: more than 80% of the viral genome from the gag to the nef genes could be determined for all sequences from South Africa, 75% of sequences from Mochudi, 60% of sequences from MRC/UVRI Uganda, and 22% of sequences from Rakai...
May 25, 2017: AIDS Research and Human Retroviruses
https://www.readbyqxmd.com/read/28537543/molecular-epidemiology-of-hepatitis-b-virus-infection-in-tanzania
#3
Joseph C Forbi, Michael Dillon, Michael A Purdy, Bakary S Drammeh, Alexandra Tejada-Strop, Daniel McGovern, Guo-Liang Xia, Yulin Lin, Lilia M Ganova-Raeva, David S Campo, Hong Thai, Gilberto Vaughan, Dunstan Haule, Regina P Kutaga, Sridhar V Basavaraju, Saleem Kamili, Yury E Khudyakov
Despite the significant public health problems associated with hepatitis B virus (HBV) in sub-Saharan Africa, many countries in this region do not have systematic HBV surveillance or genetic information on HBV circulating locally. Here, we report on the genetic characterization of 772 HBV strains from Tanzania. Phylogenetic analysis of the S-gene sequences showed prevalence of HBV genotype A (HBV/A, n=671, 86.9 %), followed by genotypes D (HBV/D, n=95, 12.3 %) and E (HBV/E, n=6, 0.8 %). All HBV/A sequences were further classified into subtype A1, while the HBV/D sequences were assigned to a new cluster...
May 25, 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28535790/clonal-replacement-of-epidemic-kpc-producing-klebsiella-pneumoniae-in-a-hospital-in-china
#4
Yuying Liang, Xiuyun Yin, Lijun Zeng, Shuiping Chen
BACKGROUND: Klebsiella pneumoniae is a frequent nosocomial pathogen causing difficult-to-treat infections worldwide. The prevalence of Klebsiella pneumoniae carbapenemase (KPC)-producing Klebsiella pneumoniae (KPC-KP) is increasing in China. The aim of this study was to investigate the molecular epidemiology of KPC-KP in a nosocomial outbreak. METHODS: Fifty-four KPC-KP isolates were consecutively collected between November 2013 and August 2014 during a KPC-KP outbreak in a tertiary care hospital in Beijing, China...
May 23, 2017: BMC Infectious Diseases
https://www.readbyqxmd.com/read/28527252/-characterization-of-clinical-isolates-of-mycobacterium-tuberculosis-from-hiv-positive-individuals-in-colombia-2012
#5
Claudia Castro, Alba Ricardo, Angie Zabaleta, Claudia Llerena, Gloria Puerto
INTRODUCTION: One third of the increase in tuberculosis cases is attributed to the spread of HIV. In 2012, 1,397 HIV-associated tuberculosis cases were reported in Colombia, i.e., 11.8% of the total cases. Molecular epidemiology tools help to understand the transmission of tuberculosis. OBJECTIVE: To characterize clinical isolates of Mycobacterium tuberculosis derived from HIV-infected individuals, received at the Laboratorio Nacional de Referencia in the Instituto Nacional de Salud...
January 24, 2017: Biomédica: Revista del Instituto Nacional de Salud
https://www.readbyqxmd.com/read/28525307/exploiting-genetic-information-to-trace-plant-virus-dispersal-in-landscapes
#6
Coralie Picard, Sylvie Dallot, Kirstyn Brunker, Karine Berthier, Phillipe Roumagnac, Samuel Soubeyrand, Emmanuel Jacquot, Gaël Thébaud
During the past decade, knowledge of pathogen life history has greatly benefited from the advent and development of molecular epidemiology. This branch of epidemiology uses information on pathogen variation at the molecular level to gain insights into a pathogen's niche and evolution and to characterize pathogen dispersal within and between host populations. Here, we review molecular epidemiology approaches that have been developed to trace plant virus dispersal in landscapes. In particular, we highlight how virus molecular epidemiology, nourished with powerful sequencing technologies, can provide novel insights at the crossroads between the blooming fields of landscape genetics, phylogeography, and evolutionary epidemiology...
May 19, 2017: Annual Review of Phytopathology
https://www.readbyqxmd.com/read/28524743/nanoparticle-exposures-from-nano-enabled-toner-based-printing-equipment-and-human-health-state-of-science-and-future-research-needs
#7
Sandra Vanessa Pirela, John Martin, Dhimiter Bello, Philip Demokritou
Toner formulations used by laser printers (LP) and photocopiers (PC), collectively called "toner-based printing equipment" (TPE), are nano-enabled products (NEP) because they contain several engineered nanomaterials (ENM) that improve toner performance. It has been shown that during consumer use (printing), these ENM are released in the air, together with other semi-volatile organic nanoparticles, and newly formed gaseous co-pollutants such as volatile organic compounds (VOC). The aim of this review is to detail and analyze physico-chemical and morphological (PCM), as well as the toxicological properties of particulate matter (PM) emissions from TPE...
May 19, 2017: Critical Reviews in Toxicology
https://www.readbyqxmd.com/read/28520983/genomic-epidemiology-of-global-vim-producing-enterobacteriaceae
#8
Yasufumi Matsumura, Gisele Peirano, Rebekah Devinney, Patricia A Bradford, Mary R Motyl, Mark D Adams, Liang Chen, Barry Kreiswirth, Johann D D Pitout
Background: : International data on the molecular epidemiology of Enterobacteriaceae with VIM carbapenemases are limited. Methods: We performed short read (Illumina) WGS on a global collection of 89 VIM-producing clinical Enterobacteriaceae (2008-14). Results: VIM-producing (11 varieties within 21 different integrons) isolates were mostly obtained from Europe. Certain integrons with bla VIM were specific to a country in different species and clonal complexes (CCs) (In 87 , In 624 , In 916 and In 1323 ), while others had spread globally among various Enterobacteriaceae species (In 110 and In 1209 )...
May 16, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/28512020/molecular-epidemiology-of-porcine-reproductive-and-respiratory-syndrome-virus-in-central-china-since-2014-the-prevalence-of-nadc30-like-prrsvs
#9
Lin-Jian Wang, Weitao Xie, Xin-Xin Chen, Songlin Qiao, Mengmeng Zhao, Yu Gu, Bao-Lei Zhao, Gaiping Zhang
Porcine reproductive and respiratory syndrome (PRRS), characterized by respiratory disorders in piglets and reproductive failure in sows, is still the great threat of swine industry. Recently, Emergence of the novel NADC30-like PRRS viruses (PRRSVs) has caused widespread outbreaks of PRRS. To investigate the epidemic characteristics of PRRSVs in Central China since 2014, 6372 clinical serum samples were tested by ELISA, 250 tissue samples were tested by RT-PCR, and among these, 30 ORF5 and 17 Nsp2 genes sequences were analyzed...
May 13, 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/28511131/genetic-diversity-and-phylogenetic-analysis-of-the-orf5-gene-of-prrsv-from-central-china
#10
Liujun Zhang, Yan Feng, Darren P Martin, Jing Chen, Sixu Ma, Pingan Xia, Gaiping Zhang
To more fully understand the genetic diversity and molecular epidemiology of prevailing porcine reproductive and respiratory syndrome virus (PRRSV) in Henan province of China, 112 full-length ORF5 gene sequences, originating from Henan province between 2006 and 2015, were subjected to sequence variation and phylogenetic analysis. Phylogenetic analysis revealed that all Henan isolates belonged to the Type 2 genotype and could be further divided into three subgroups. Subgroup 1 and 2 viruses predominated in Henan and subgroup 2 overtook subgroup 1 as the most prevalent PRRSV between 2006 and 2015...
May 11, 2017: Research in Veterinary Science
https://www.readbyqxmd.com/read/28509842/molecular-epidemiology-of-methicillin-resistant-and-methicillin-susceptible-staphylococcus-aureus-in-the-ovine-dairy-chain-and-in-farm-related-humans
#11
Guerrino Macori, Giuseppina Giacinti, Alberto Bellio, Silvia Gallina, Daniela Manila Bianchi, Daniele Sagrafoli, Nicla Marri, Gilberto Giangolini, Simonetta Amatiste, Lucia Decastelli
Staphylococcus aureus is a major cause of clinical infections in humans and its enterotoxins cause foodborne disease. In the present study, we tested a total of 51 isolates of S. aureus from small-ruminant dairy farms with artisan dairy facilities, all located in Latium, Italy. The farms have a known history of a high prevalence of methicillin-resistant S. aureus (MRSA). Most of the MRSA isolates (27 of 51) belonged to spa-type t127 (43.1%), followed by t2678 (3.9%), t044 (2%), t1166 (2%), and t1773 (2%). PFGE performed on mecA positive strains identified one cluster (≥ 80% of similarity), comprising 22 MRSA...
May 16, 2017: Toxins
https://www.readbyqxmd.com/read/28502480/stenotrophomonas-maltophilia-in-a-university-hospital-of-traditional-chinese-medicine-molecular-epidemiology-and-antimicrobial-resistance
#12
S Zhao, L Yang, H Liu, F Gao
Stenotrophomona maltophilia has emerged as an important opportunistic pathogen that is highly antibiotic resistant. Analysis of antibiotic susceptibilities, drug-resistant gene profiles and molecular typing of S. maltophilia was undertaken in a university hospital of traditional Chinese medicine in East China. Resistance to sulphamethoxazole (SXT) was found to be an indicator of multi-drug resistance. SXT resistance was mediated by sul and dfrA genes in integrons, especially class 1. Some evidence of clonal dissemination was found, indicating the occurrence of cross-transmission of antibiotic-resistant strains within the hospital...
April 7, 2017: Journal of Hospital Infection
https://www.readbyqxmd.com/read/28502018/evolutionary-processes-in-populations-of-cryptosporidium-inferred-from-gp60-sequence-data
#13
Juan C Garcia-R, David T S Hayman
Cryptosporidiosis is one of the most common human infectious diseases globally. The gp60 gene has been adopted as a key marker for molecular epidemiological investigations into this protozoan disease because of the capability to characterize genotypes and detect variants within Cryptosporidium species infecting humans. However, we know relatively little about the potential spatial and temporal variation in population demography that can be inferred from this gene beyond that it is recognized to be under selective pressure...
May 13, 2017: Parasitology Research
https://www.readbyqxmd.com/read/28500748/epidemiology-and-genetic-diversity-of-classic-human-astrovirus-among-hospitalized-children-with-acute-gastroenteritis-in-uruguay
#14
Lfl Tort, A Lizasoain, M Victoria, C Papalardo, S Castro, E Arreseigor, P Lopez, R Colina
Classic Human Astrovirus (Classic HAstV) are one of the most important causes of pediatric acute gastroenteritis (AGE), after rotaviruses and arguably caliciviruses. The aim of this study was to determine the molecular epidemiology of Classic HAstV from 175 clinical samples, being 153 stools and 22 vomits, collected from pediatric hospitalized patients with AGE in Salto city, Uruguay, from January 2011 to December 2012. Classic HAstV were detected and genotyped by using a qualitative Retro Transcription - Polimerase Chain Reaction (RT-PCR) directed to the Open Reading Frame-2 (ORF2) region C...
May 13, 2017: Journal of Medical Virology
https://www.readbyqxmd.com/read/28494612/oxidative-stress-and-inflammation-induced-by-environmental-and-psychological-stressors-a-biomarker-perspective
#15
Pietro Ghezzi, Luciano Floridi, Diana Boraschi, Antonio Cuadrado, Gina Manda, Snezana Levic, Fulvio D'Acquisto, Alice Laura Hamilton, Toby Athersuch, Liza Selley
SIGNIFICANCE: The environment can elicit biological responses such as oxidative stress (OS) and inflammation as consequence of chemical, physical or psychological changes. As population studies are essential for establishing these environment-organism interactions, biomarkers of oxidative stress or inflammation are critical in formulating mechanistic hypotheses. Recent advances. By using examples of stress induced by various mechanisms, we focus on the biomarkers that have been used to assess oxidative stress and inflammation in these conditions...
May 11, 2017: Antioxidants & Redox Signaling
https://www.readbyqxmd.com/read/28489920/a-national-study-of-the-molecular-epidemiology-of-hiv-1-in-australia-2005-2012
#16
Alison Castley, Shailendra Sawleshwarkar, Rick Varma, Belinda Herring, Kiran Thapa, Dominic Dwyer, Doris Chibo, Nam Nguyen, Karen Hawke, Rodney Ratcliff, Roger Garsia, Anthony Kelleher, David Nolan
INTRODUCTION: Rates of new HIV-1 diagnoses are increasing in Australia, with evidence of an increasing proportion of non-B HIV-1 subtypes reflecting a growing impact of migration and travel. The present study aims to define HIV-1 subtype diversity patterns and investigate possible HIV-1 transmission networks within Australia. METHODS: The Australian Molecular Epidemiology Network (AMEN) HIV collaborating sites in Western Australia, South Australia, Victoria, Queensland and western Sydney (New South Wales), provided baseline HIV-1 partial pol sequence, age and gender information for 4,873 patients who had genotypes performed during 2005-2012...
2017: PloS One
https://www.readbyqxmd.com/read/28482417/-molecular-epidemiologic-study-on-mycobacterium-tuberculosis-from-drug-resistance-monitoring-sites-of-guangdong-province-2015
#17
X C Huang, H X Guo, Z H Wu, C X Guo, W J Wei, H C Li, Q Sun, C C Zhang, Z Y Li, T Chen, Q Zhong, L Zhou
Objective: To understand the characteristics of Mycobacterium tuberculosis (MTB) in epidemiology and distribution from Guangdong Province, and to explore the risk factors associated with drug resistance. Methods: A total of 225 clinical strains of MTB collected from 5 drug resistance monitoring sites of Guangdong Province in 2015 were tested by Regions of Difference 105 (RD105) deletion test and 15 loci mycobacterial interspersed repetitive units (MIRU) were used for genotyping. Gene clustering was analyzed using BioNumerics7...
May 12, 2017: Chinese Journal of Tuberculosis and Respiratory Diseases
https://www.readbyqxmd.com/read/28481953/molecular-epidemiological-survey-of-bacteremia-by-multidrug-resistant-pseudomonas-aeruginosa-the-relevance-of-intrinsic-resistance-mechanisms
#18
Raquel Cristina Cavalcanti Dantas, Rebecca Tavares E Silva, Melina Lorraine Ferreira, Iara Rossi Gonçalves, Bruna Fuga Araújo, Paola Amaral de Campos, Sabrina Royer, Deivid William da Fonseca Batistão, Paulo Pinto Gontijo-Filho, Rosineide Marques Ribas
The bacterial factors associated with bacteremia by multidrug-resistant and extensively drug-resistant P. aeruginosa, including overexpression of efflux pumps, AmpC overproduction, and loss/alteration of the OprD porin in isolates that are non-Metallo-β-Lactamase producing were analyzed in a retrospective study. Molecular analyses included strain typing by Pulsed Field Gel Electrophoresis and identification of key genes via qualitative and quantitative PCR-based assays. Previous use of carbapenems and tracheostomy was independently associated with the development of bacteremia by extensively drug-resistant and multidrug-resistant strains of P...
2017: PloS One
https://www.readbyqxmd.com/read/28481275/porcine-circovirus-type-2-pcv2-vaccines-in-the-context-of-current-molecular-epidemiology
#19
REVIEW
Anbu K Karuppannan, Tanja Opriessnig
Porcine circovirus type 2 (PCV2) is an economically important swine pathogen and, although small, it has the highest evolution rate among DNA viruses. Since the discovery of PCV2 in the late 1990s, this minimalistic virus with a 1.7 kb single-stranded DNA genome and two indispensable genes has become one of the most important porcine pathogens, and presently is subjected to the highest volume of prophylactic intervention in the form of vaccines in global swine production. PCV2 can currently be divided into five different genotypes, PCV2a through PCV2e...
May 6, 2017: Viruses
https://www.readbyqxmd.com/read/28481120/molecular-epidemiology-of-wu-polyomavirus-in-hospitalized-children-with-acute-respiratory-tract-infection-in-china
#20
Teng Zhu, Qing-Bin Lu, Shu-Yan Zhang, Ying Wo, Lu Zhuang, Pan-He Zhang, Xiao-Ai Zhang, Wei Wei, Wei Liu
AIM: To explore the molecular epidemiology and clinical characteristics of Washington University polyomavirus (WUPyV) infection in pediatric patients with acute respiratory tract infections in China. MATERIALS & METHODS: A laboratory surveillance was performed to recruit pediatric patients with acute respiratory tract infections. WUPyV was detected using real-time PCR and complete genome was sequenced for randomly selected positive nasopharyngeal aspirate. RESULTS: Altogether 122 (7...
May 8, 2017: Future Microbiology
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