A large-scale stochastic spatiotemporal model for Aedes albopictus-borne chikungunya epidemiology

Chikungunya is a viral disease transmitted to humans primarily via the bites of infected Aedes mosquitoes. The virus caused a major epidemic in the Indian Ocean in 2004, affecting millions of inhabitants, while cases have also been observed in Europe since 2007. We developed a stochastic spatiotemporal model of Aedes albopictus-borne chikungunya transmission based on our recently developed environmentally-driven vector population dynamics model. We designed an integrated modelling framework incorporating large-scale gridded climate datasets to investigate disease outbreaks on Reunion Island and in Italy. We performed Bayesian parameter inference on the surveillance data, and investigated the validity and applicability of the underlying biological assumptions. The model successfully represents the outbreak and measures of containment in Italy, suggesting wider applicability in Europe. In its current configuration, the model implies two different viral strains, thus two different outbreaks, for the two-stage Reunion Island epidemic. Characterisation of the posterior distributions indicates a possible relationship between the second larger outbreak on Reunion Island and the Italian outbreak. The model suggests that vector control measures, with different modes of operation, are most effective when applied in combination: adult vector intervention has a high impact but is short-lived, larval intervention has a low impact but is long-lasting, and quarantining infected territories, if applied strictly, is effective in preventing large epidemics. We present a novel approach in analysing chikungunya outbreaks globally using a single environmentally-driven mathematical model. Our study represents a significant step towards developing a globally applicable Ae. albopictus-borne chikungunya transmission model, and introduces a guideline for extending such models to other vector-borne diseases

Filling in the gaps: estimating numbers of chlamydia tests and diagnoses by age group and sex before and during the implementation of the English National Screening Programme, 2000 to 2012.

To inform mathematical modelling of the impact of chlamydia screening in England since 2000, a complete picture of chlamydia testing is needed. Monitoring and surveillance systems evolved between 2000 and 2012. Since 2012, data on publicly funded chlamydia tests and diagnoses have been collected nationally. However, gaps exist for earlier years. We collated available data on chlamydia testing and diagnosis rates among 15-44-year-olds by sex and age group for 2000-2012. Where data were unavailable, we applied data- and evidence-based assumptions to construct plausible minimum and maximum estimates and set bounds on uncertainty. There was a large range between estimates in years when datasets were less comprehensive (2000-2008); smaller ranges were seen hereafter. In 15-19-year-old women in 2000, the estimated diagnosis rate ranged between 891 and 2,489 diagnoses per 100,000 persons. Testing and diagnosis rates increased between 2000 and 2012 in women and men across all age groups using minimum or maximum estimates, with greatest increases seen among 15-24-year-olds. Our dataset can be used to parameterise and validate mathematical models and serve as a reference dataset to which trends in chlamydia-related complications can be compared. Our analysis highlights the complexities of combining monitoring and surveillance datasets

Primer concentration and Pre-denaturation Time Effect on cyt-K Bacillus cereus Detection using Real-Time PCR Method

Foodborne disease is a global threat that can affect all sections of society, both in developed or developing countries. Bacillus cereus is a Gram-positive bacteria that can cause food poisoning disease in humans. [2] Real-Time PCR detection method is one of the molecular marker methods that has been widely recognized as a fast, reliable, sensitive and specific detection tool for detecting pathogenic bacteria. In previous studies, the optimum condition and formulas applied for cyt-K 2 primer pairs have been obtained using Real-Time PCR. The purpose of this study is to find out the best conditions work of the primer pair cyt-K Bacillus cereus on detecting bacteria target using variations of pre-denaturation time and primer concentration with Real-Time PCR method. The annealing temperature used for PCR is at 60°C with sample concentration 50 ng/µL of B. cereus. Real-time PCR detection of variations in pre-denaturation time and primer concentration obtained the best conditions for primer pair cyt-K work at minute 4 with a primer concentration of 10 pmol and successfully amplifying the target by producing a Ct value of B. cereus at 13.04. Based on the results of the study, the primer pair cyt-K were reproducible in detecting the target gene and in the further step, this research can be continued to developed a prototype detection kit for foodborne pathogen bacteria using Real-Time PCR method

Factors associated with delayed presentation to healthcare facilities for Lassa fever cases, Nigeria 2019: a retrospective cohort study.

BACKGROUND: Large outbreaks of Lassa fever (LF) occur annually in Nigeria. The case fatality rate among hospitalised cases is ~ 20%. The antiviral drug ribavirin along with supportive care and rehydration are the recommended treatments but must be administered early (within 6 days of symptom onset) for optimal results. We aimed to identify factors associated with late presentation of LF cases to a healthcare facility to inform interventions. METHODS: We undertook a retrospective cohort study of all laboratory confirmed LF cases reported in Nigeria from December 2018 to April 2019. We performed descriptive epidemiology and a univariate Cox proportional-hazards regression analysis to investigate the effect of clinical (symptom severity), epidemiological (age, sex, education, occupation, residential State) and exposure (travel, attendance at funeral, exposure to rodents or confirmed case) factors on time to presentation. RESULTS: Of 389 cases, median presentation time was 6 days (IQR 4-10 days), with 53% attending within 6 days. There were no differences in presentation times by sex but differences were noted by age-group; 60+ year-olds had the longest delays while 13-17 year-olds had the shortest. By sex and age, there were differences seen among the younger ages, with 0-4-year-old females presenting earlier than males (4 days and 73% vs. 10 days and 30%). For 5-12 and 13-17 year-olds, males presented sooner than females (males: 5 days, 65% and 3 days, 85% vs. females: 6 days, 50% and 5 days, 61%, respectively). Presentation times differed across occupations 4.5-9 days and 20-60%, transporters (people who drive informal public transport vehicles) had the longest delays. Other data were limited (41-95% missing). However, the Cox regression showed no factors were statistically associated with longer presentation time. CONCLUSIONS: Whilst we observed important differences in presentation delays across factors, our sample size was insufficient to show any statistically significant differences that might exist. However, almost half of cases presented after 6 days of onset, highlighting the need for more accurate and complete surveillance data to determine if there is a systemic or specific cause for delays, so to inform, monitor and evaluate public health strategies and improve outcomes

Detection of Salmonella typhimurium on artificially contaminated milk by real time PCR using STM4497 and fljB primers

Detection of food-borne bacterial pathogens was developed to overcome the limitations. The aim of this research was to develop Salmonella typhimurium detection by Real Time Polymerase Chain Reaction (RT-PCR) using two pairs of primers. The ability of primer pairs to detect S. typhimurium is seen from cycle threshold or Ct. Artificially contaminated milk sample with 24 ng each microliter can be detected with fljB (flagellin gene) primers on Ct 12,933 and with STM4497 (hypothetical protein code) primers on Ct 13,665. The specificity test of both primers showed that melting temperature (Tm) of fljB was 80,5 degree Celsius, and STM449 was 81,6 degree Celsius. FljB and STM4497 primers gave an average detection limit respectively of 11,75 Colony Forming Unit (CFU) each milliliter and 6,8 CFU each milliliter. The time needed throughout the detection process of S. typhimurium with fljB and STM4497 primers is faster than conventional methods. Based on the results it can be concluded that primers fljB and STM449 S. typhimurium can be applied to detection and quantification of S. typhimurium in milk samples

Outbreak management strategies for Italy.

<p>Median, red line, and 95% range, red shade, of epidemic trajectories are plotted together with adult abundance, blue line, and incidence reports, dark circles [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0174293#pone.0174293.ref007" target="_blank">7</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0174293#pone.0174293.ref009" target="_blank">9</a>]. The vector control measures reported in the literature [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0174293#pone.0174293.ref007" target="_blank">7</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0174293#pone.0174293.ref009" target="_blank">9</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0174293#pone.0174293.ref040" target="_blank">40</a>] were implemented in (a). Only adulticide treatment was implemented in (b). A stronger control strategy on the immature stages and breeding sites was implemented in (c). The effect of perfectly isolating the symptomatic cases is shown in (d) with a black line, median, and a grey shade, 95% range. The red dashed horizontal line indicate the median outbreak impact (1700 human infections) without intervention.</p

The rate of human-vector interactions.

<p>The plot shows the daily average number of human-vector interactions as modelled using the standard approach (<i>λ</i>_<i>V</i>, see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0174293#sec002" target="_blank">Methods</a>) or by incorporating humans as a limiting factor (2<i>λ</i>_<i>V</i> <i>λ</i>_<i>H</i>/(<i>λ</i>_<i>V</i> + <i>λ</i>_<i>H</i>), see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0174293#sec002" target="_blank">Methods</a>) in the presence of 1 and 100 humans.</p

Model parameters with reference intervals obtained from literature.

<p>Model parameters with reference intervals obtained from literature.</p

Outbreaks of <i>Ae. albopictus</i>-borne chikungunya in Italy and on Reunion Island.

<p>(a) Number of reported, and laboratory confirmed, infections in Ravenna, Italy, during the chikungunya outbreak in 2007 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0174293#pone.0174293.ref009" target="_blank">9</a>]. (b) Total number of infections reported by the island-wide surveillance system on Reunion Island during 2005-2006 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0174293#pone.0174293.ref036" target="_blank">36</a>]. The horizontal lines in (a, b) indicate the time frames and infections that each dataset covers. (c) The centroids of the patches of the metapopulation model for Reunion Island.</p

Prediction of adult vector abundance and activity in Italy and on Reunion Island.

<p>(a) The predicted number of eggs per ovitrap per week in Castiglione di Cervia and Castiglione di Ravenna villages is shown with the surveillance data from four neighbouring towns [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0174293#pone.0174293.ref079" target="_blank">79</a>]: Cesena (circle), Forli (triangle), Ravenna (square), and Rimini (diamond). The beginning and end of the outbreak and the time of application of vector control measures [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0174293#pone.0174293.ref007" target="_blank">7</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0174293#pone.0174293.ref009" target="_blank">9</a>] are marked in the figure. The predicted vector abundance is scaled down to 75% in the plot. (b) Predicted adult female vector abundance per ovitrap in the two regions for a time frame covering both the Italian and the Reunion Island outbreaks. (c) Predicted daily fecundity during the same time frame in the two regions. The pale grey shades in (a, b, c) indicate the 95% credible interval of the mean.</p