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Outbreak prediction

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https://www.readbyqxmd.com/read/29329455/serologic-evidence-of-ebolavirus-infection-in-a-population-with-no-history-of-outbreaks-in-the-democratic-republic-of-the-congo
#1
Sabue Mulangu, Vivian H Alfonso, Nicole A Hoff, Reena H Doshi, Prime Mulembakani, Neville K Kisalu, Emile Okitolonda-Wemakoy, Benoit Ilunga Kebela, Hadar Marcus, Joseph Shiloach, Je Nie Phue, Linda L Wright, Jean-Jacques Muyembe-Tamfum, Nancy J Sullivan, Anne W Rimoin
Background: Previous studies suggest that cases of Ebola virus disease (EVD) may go unreported because they are asymptomatic or unrecognized, but evidence is limited by study designs and sample size. Methods: A large population-based survey was conducted (n = 3415) to assess animal exposures and behaviors associated with Ebolavirus antibody prevalence in rural Kasai Oriental province of the Democratic Republic of Congo (DRC). Fourteen villages were randomly selected and all healthy individuals ≥1 year of age were eligible...
January 10, 2018: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/29324655/evaluation-of-an-accelerated-workflow-for-surveillance-of-esbl-ctx-m-producing-escherichia-coli-using-amplicon-based-next-generation-sequencing-and-automated-analysis
#2
Nilay Peker, John W A Rossen, Ruud H Deurenberg, Paula C Langereis, Erwin G C Raangs, Jan A Kluytmans, Alexander W Friedrich, Jacobien Veenemans, Bhanu Sinha
Outbreak management of extended spectrum β-lactamase (ESBL)-producing pathogens requires rapid and accurate diagnosis. However, conventional screening is slow and labor-intensive. The vast majority of the screened samples are negative and detection of non-outbreak-related resistant micro-organisms often complicates outbreak management. In a CTX-M-15-producing Escherichia coli outbreak, 149 fecal samples and rectal eSwabs were collected by a cross-sectional survey in a Dutch nursing home. Samples were processed by routine diagnostic methods...
January 11, 2018: Microorganisms
https://www.readbyqxmd.com/read/29305180/epidemic-spreading-dynamics-with-drug-resistance-and-heterogeneous-contacts
#3
Peng-Bi Cui, Lei Gao, Wei Wang
Drug resistance and strong contacts actually play crucial roles in epidemic spread in complex systems. Nevertheless, neither theoretical model or methodology is proposed to address this. We thus consider an edge-based epidemic spread model considering the two key ingredients, in which the contacts are grouped into two classes: strong contacts and normal ones. Next, we present a unified edge-based compartmental approach to the spread dynamics on Erdös-Rényi (ER) networks and validate its results by extensive numerical simulations...
January 2, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29301048/spatial-displacement-of-a-lure-component-can-reduce-catches-of-two-nontarget-species-during-spring-monitoring-of-southern-pine-beetle
#4
William P Shepherd, Brian T Sullivan
Local outbreak risk for the southern pine beetle, Dendroctonus frontalis Zimmermann (Coleoptera: Curculionidae), is forecast with a trapping survey conducted every spring throughout the southeastern United States. Traps baited with pine odors and components of the D. frontalis aggregation pheromone are used to obtain abundance estimates of both this species and its clerid predator Thanasimus dubius (F.) (Coleoptera: Cleridae); these data are entered into a predictive model that estimates outbreak risk. An attractant synergist for D...
January 1, 2018: Journal of Insect Science
https://www.readbyqxmd.com/read/29290644/interactions-of-predominant-insects-and-diseases-with-climate-change-in-douglas-fir-forests-of-western-oregon-and-washington-u-s-a
#5
Michelle C Agne, Peter A Beedlow, David C Shaw, David R Woodruff, E Henry Lee, Steven P Cline, Randy L Comeleo
Forest disturbance regimes are beginning to show evidence of climate-mediated changes, such as increasing severity of droughts and insect outbreaks. We review the major insects and pathogens affecting the disturbance regime for coastal Douglas-fir forests in western Oregon and Washington State, USA, and ask how future climate changes may influence their role in disturbance ecology. Although the physiological constraints of light, temperature, and moisture largely control tree growth, episodic and chronic disturbances interacting with biological factors have substantial impacts on the structure and functioning of forest ecosystems in this region...
February 1, 2018: Forest Ecology and Management
https://www.readbyqxmd.com/read/29288541/can-ebola-virus-evolve-to-be-less-virulent-in-humans
#6
Mircea T Sofonea, Lafi Aldakak, Luis Fernando Boullosa, Samuel Alizon
Understanding Ebola Virus (EBOV) virulence evolution is not only timely but also raises specific questions because it causes one of the most virulent human infections and it is capable of transmission after the death of its host. Using a compartmental epidemiological model that captures three transmission routes (by regular contact, via dead bodies and by sexual contact), we infer the evolutionary dynamics of case fatality ratio (CFR) on the scale of an outbreak and on the long term. Our major finding is that the virus's specific life cycle imposes selection for high levels of virulence and that this pattern is robust to parameter variations in biological ranges...
December 29, 2017: Journal of Evolutionary Biology
https://www.readbyqxmd.com/read/29280264/anti-shigatoxin-2-antibodies-in-ehec-o104-h4-infected-patients-may-predict-hemolytic-uremic-syndrome
#7
Werner Dammermann, Valentin Mihajlov, Barbara Middendorf, Alexander Mellmann, Helge Karch, Stefan Lüth, Sebastian Ullrich
BACKGROUND AND AIM: An outbreak of Shigatoxin 2 (Stx2) producing enterohemorrhagic and enteroaggregative E.coli (EHEC) O104:H4 infection in May 2011 in Germany caused enterocolitis and an unprecedented high 22% rate of hemolytic uremic syndrome (HUS). We hypothesized that anti-Stx2 IgM or IgG titers might predict HUS development. METHODS: 32 patients infected with EHEC O104:H4 (HUS: n=23;non-HUS: n=9) were retrospectively screened for anti-Stx2 IgM/IgG and matched with clinical data regarding HUS development, fever, superinfection, dialysis, neurological symptoms, intensive care, antibiotic treatment, and plasmapheresis...
December 27, 2017: Journal of Gastroenterology and Hepatology
https://www.readbyqxmd.com/read/29275190/molecular-characterization-of-genomic-dna-in-mycoplasma-pneumoniae-strains-isolated-from-serious-mycoplasma-pneumonia-cases-in-2016-yunnan-china
#8
Lijuan Qiu, Lin Wang, Li Tan, Ming Li, Chengqing Wu, Li Li, Zhen Zhang, Hongchao Jiang, Qiangming Sun, Tiesong Zhang
Mycoplasma pneumoniae (MP) is particularly prevalent in low-immunity school-age children. Few data have been reported on MP prevalence in Yunnan, China. This study was designed to investigate the prevalence and characterize genomic DNA of MP in a small outbreak in 2016, Southwest China. RepMP4 and RepMP2/3 genes of MP positive samples were amplified for molecular typing through sequence alignment and PCR-RFLP assay. Phylogenetic trees were constructed by MEGA5.0. The results showed that two distinct P1 types (type I and type II) were prevalent in this MP outbreak...
December 22, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29250046/the-emerging-fish-pathogen-flavobacterium-spartansii-isolated-from-chinook-salmon-comparative-genome-analysis-and-molecular-manipulation
#9
Shicheng Chen, Jochen Blom, Thomas P Loch, Mohamed Faisal, Edward D Walker
Flavobacterium spartansii strain T16T was isolated from a disease outbreak in hatchery-reared Chinook salmon (Oncorhynchus tshawytscha) fingerlings. To gain insight into its genomic content, structure and virulence pathogenesis factors, comparative genome analyses were performed using genomes from environmental and virulent Flavobacterium strains. F. spartansii shared low average nucleotide identity (ANI) to well-known fish-pathogenic flavobacteria (e.g., F. columnare, F. psychrophilum, and F. branchiophilum), indicating that it is a new and emerging fish pathogen...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29247013/whole-genome-sequencing-reveals-transmission-of-gonococcal-antibiotic-resistance-among-men-who-have-sex-with-men-an-observational-study
#10
Jason C Kwong, Eric P F Chow, Kerrie Stevens, Timothy P Stinear, Torsten Seemann, Christopher K Fairley, Marcus Y Chen, Benjamin P Howden
OBJECTIVES: Drug-resistant Neisseria gonorrhoeae are now a global public health threat. Direct transmission of antibiotic-resistant gonococci between individuals has been proposed as a driver for the increased transmission of resistance, but direct evidence of such transmission is limited. Whole-genome sequencing (WGS) has superior resolution to investigate outbreaks and disease transmission compared with traditional molecular typing methods such as multilocus sequence typing (MLST) and N...
December 15, 2017: Sexually Transmitted Infections
https://www.readbyqxmd.com/read/29241658/spatiotemporal-bayesian-networks-for-malaria-prediction
#11
Peter Haddawy, A H M Imrul Hasan, Rangwan Kasantikul, Saranath Lawpoolsri, Patiwat Sa-Angchai, Jaranit Kaewkungwal, Pratap Singhasivanon
Targeted intervention and resource allocation are essential for effective malaria control, particularly in remote areas, with predictive models providing important information for decision making. While a diversity of modeling technique have been used to create predictive models of malaria, no work has made use of Bayesian networks. Bayes nets are attractive due to their ability to represent uncertainty, model time lagged and nonlinear relations, and provide explanations. This paper explores the use of Bayesian networks to model malaria, demonstrating the approach by creating village level models with weekly temporal resolution for Tha Song Yang district in northern Thailand...
December 11, 2017: Artificial Intelligence in Medicine
https://www.readbyqxmd.com/read/29240665/airborne-or-fomite-transmission-for-norovirus-a-case-study-revisited
#12
Shenglan Xiao, Julian W Tang, Yuguo Li
Norovirus infection, a highly prevalent condition associated with a high rate of morbidity, comprises a significant health issue. Although norovirus transmission mainly occurs via the fecal-oral and vomit-oral routes, airborne transmission has been proposed in recent decades. This paper re-examines a previously described norovirus outbreak in a hotel restaurant wherein airborne transmission was originally inferred. Specifically, the original evidence that suggested airborne transmission was re-analyzed by exploring an alternative hypothesis: could this outbreak instead have occurred via fomite transmission? This re-analysis was based on whether fomite transmission could have yielded similar attack rate distribution patterns...
December 14, 2017: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/29238900/forecasting-the-2001-foot-and-mouth-disease-epidemic-in-the-uk
#13
David W Shanafelt, Glyn Jones, Mauricio Lima, Charles Perrings, Gerardo Chowell
Near real-time epidemic forecasting approaches are needed to respond to the increasing number of infectious disease outbreaks. In this paper, we retrospectively assess the performance of simple phenomenological models that incorporate early sub-exponential growth dynamics to generate short-term forecasts of the 2001 foot-and-mouth disease epidemic in the UK. For this purpose, we employed the generalized-growth model (GGM) for pre-peak predictions and the generalized-Richards model (GRM) for post-peak predictions...
December 13, 2017: EcoHealth
https://www.readbyqxmd.com/read/29238330/an-assessment-of-different-genomic-approaches-for-inferring-phylogeny-of-listeria-monocytogenes
#14
Clémentine Henri, Pimlapas Leekitcharoenphon, Heather A Carleton, Nicolas Radomski, Rolf S Kaas, Jean-François Mariet, Arnaud Felten, Frank M Aarestrup, Peter Gerner Smidt, Sophie Roussel, Laurent Guillier, Michel-Yves Mistou, René S Hendriksen
Background/objectives: Whole genome sequencing (WGS) has proven to be a powerful subtyping tool for foodborne pathogenic bacteria like L. monocytogenes. The interests of genome-scale analysis for national surveillance, outbreak detection or source tracking has been largely documented. The genomic data however can be exploited with many different bioinformatics methods like single nucleotide polymorphism (SNP), core-genome multi locus sequence typing (cgMLST), whole-genome multi locus sequence typing (wgMLST) or multi locus predicted protein sequence typing (MLPPST) on either core-genome (cgMLPPST) or pan-genome (wgMLPPST)...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29237604/stormy-weather-a-retrospective-analysis-of-demand-for-emergency-medical-services-during-epidemic-thunderstorm-asthma
#15
Emily Andrew, Ziad Nehme, Stephen Bernard, Michael J Abramson, Ed Newbigin, Ben Piper, Justin Dunlop, Paul Holman, Karen Smith
OBJECTIVES: To describe the demand for emergency medical assistance during the largest outbreak of thunderstorm asthma reported globally, which occurred on 21 November 2016. DESIGN: A time series analysis was conducted of emergency medical service caseload between 1 January 2015 and 31 December 2016. Demand during the thunderstorm asthma event was compared to historical trends for the overall population and across specific subgroups. SETTING: Victoria, Australia...
December 13, 2017: BMJ: British Medical Journal
https://www.readbyqxmd.com/read/29237401/six-monthly-appointment-spacing-for-clinical-visits-as-a-model-for-retention-in-hiv-care-in-conakry-guinea-a-cohort-study
#16
Cavin Epie Bekolo, Abdourahimi Diallo, Mit Philips, Joseph-Desire Yuma, Letizia Di Stefano, Stéphanie Drèze, Jerome Mouton, Youssouf Koita, Ousseni W Tiomtore
BACKGROUND: The outbreak of the Ebola virus disease (EVD) in 2014 led to massive dropouts in HIV care in Guinea. Meanwhile, Médecins Sans Frontières (MSF) was implementing a six-monthly appointment spacing approach adapted locally as Rendez-vous de Six Mois (R6M) with an objective to improve retention in care. We sought to evaluate this innovative model of ART delivery in circumstances where access to healthcare is restricted. METHODS: A retrospective cohort study in 2014 of the outcome of a group of stable patients (viral load ≤1000 copies/μl) enrolled voluntarily in R6M compared with a group of stable patients continuing standard one to three monthly visits in Conakry...
December 13, 2017: BMC Infectious Diseases
https://www.readbyqxmd.com/read/29234082/rebound-of-cotton-leaf-curl-multan-virus-and-its-exclusive-detection-in-cotton-leaf-curl-disease-outbreak-punjab-india-2015
#17
Sibnarayan Datta, Raghvendra Budhauliya, Bidisha Das, Reji Gopalakrishnan, Sonika Sharma, Soumya Chatterjee, Vanlalhmuaka, P Srinivas Raju, Vijay Veer
Cotton leaf curl disease (CLCuD) outbreaks caused by CLCuD associated begomoviruses (CABs) significantly constrain cotton production in India and Pakistan. In comparison to the CABs circulating in Pakistan, molecular epidemiology, evolution and recombination patterns of CABs circulating in India are less studied. In this work, we characterized CAB complex sequences obtained from the most recent outbreak (Punjab, India, 2015), and rigorously analyzed them with reference to GenBank sequences, submitted from India, Pakistan and other neighbouring countries, using contemporary bioinformatics approaches...
December 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29232561/development-of-artificial-intelligence-approach-to-forecasting-oyster-norovirus-outbreaks-along-gulf-of-mexico-coast
#18
Shima Shamkhali Chenar, Zhiqiang Deng
This paper presents an artificial intelligence-based model, called ANN-2Day model, for forecasting, managing and ultimately eliminating the growing risk of oyster norovirus outbreaks. The ANN-2Day model was developed using Artificial Neural Network (ANN) Toolbox in MATLAB Program and 15-years of epidemiological and environmental data for six independent environmental predictors including water temperature, solar radiation, gage height, salinity, wind, and rainfall. It was found that oyster norovirus outbreaks can be forecasted with two-day lead time using the ANN-2Day model and daily data of the six environmental predictors...
December 9, 2017: Environment International
https://www.readbyqxmd.com/read/29230614/translating-predictions-of-zoonotic-viruses-for-policymakers
#19
Seth D Judson, Matthew LeBreton, Trevon Fuller, Risa M Hoffman, Kevin Njabo, Timothy F Brewer, Elsa Dibongue, Joseph Diffo, Jean-Marc Feussom Kameni, Severin Loul, Godwin W Nchinda, Richard Njouom, Julius Nwobegahay, Jean Michel Takuo, Judith N Torimiro, Abel Wade, Thomas B Smith
Recent outbreaks of Ebola virus disease and Zika virus disease highlight the need for disseminating accurate predictions of emerging zoonotic viruses to national governments for disease surveillance and response. Although there are published maps for many emerging zoonotic viruses, it is unknown if there is agreement among different models or if they are concordant with national expert opinion. Therefore, we reviewed existing predictions for five high priority emerging zoonotic viruses with national experts in Cameroon to investigate these issues and determine how to make predictions more useful for national policymakers...
December 11, 2017: EcoHealth
https://www.readbyqxmd.com/read/29230364/complete-genome-sequence-and-comparative-genomics-of-the-golden-pompano-trachinotus-ovatus-pathogen-vibrio-harveyi-strain-qt520
#20
Zhigang Tu, Hongyue Li, Xiang Zhang, Yun Sun, Yongcan Zhou
Vibrio harveyi is a Gram-negative, halophilic bacterium that is an opportunistic pathogen of commercially farmed marine vertebrate species. To understand the pathogenicity of this species, the genome of V. harveyi QT520 was analyzed and compared to that of other strains. The results showed the genome of QT520 has two unique circular chromosomes and three endogenous plasmids, totaling 6,070,846 bp with a 45% GC content, 5,701 predicted ORFs, 134 tRNAs and 37 rRNAs. Common virulence factors, including ACF, IlpA, OmpU, Flagellin, Cya, Hemolysin and MARTX, were detected in the genome, which are likely responsible for the virulence of QT520...
2017: PeerJ
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