Evaluation of WGS-subtyping methods for epidemiological surveillance of foodborne salmonellosis

Background: Salmonellosis is one of the most common foodborne diseases worldwide. Although human infection by non-typhoidal Salmonella (NTS) enterica subspecies enterica is associated primarily with a self-limiting diarrhoeal illness, invasive bacterial infections (such as septicaemia, bacteraemia and meningitis) were also reported. Human outbreaks of NTS were reported in several countries all over the world including developing as well as high-income countries. Conventional laboratory methods such as pulsed field gel electrophoresis (PFGE) do not display adequate discrimination and have their limitations in epidemiological surveillance. It is therefore very crucial to use accurate, reliable and highly discriminative subtyping methods for epidemiological characterisation and outbreak investigation. Methods: Here, we used different whole genome sequence (WGS)-based subtyping methods for retrospective investigation of two different outbreaks of Salmonella Typhimurium and Salmonella Dublin that occurred in 2013 in UK and Ireland respectively. Results: Single nucleotide polymorphism (SNP)-based cluster analysis of Salmonella Typhimurium genomes revealed well supported clades, that were concordant with epidemiologically defined outbreak and confirmed the source of outbreak is due to consumption of contaminated mayonnaise. SNP-analyses of Salmonella Dublin genomes confirmed the outbreak however the source of infection could not be determined. The core genome multilocus sequence typing (cgMLST) was discriminatory and separated the outbreak strains of Salmonella Dublin from the non-outbreak strains that were concordant with the epidemiological data however cgMLST could neither discriminate between the outbreak and non-outbreak strains of Salmonella Typhimurium nor confirm that contaminated mayonnaise is the source of infection, On the other hand, other WGS-based subtyping methods including multilocus sequence typing (MLST), ribosomal MLST (rMLST), whole genome MLST (wgMLST), clustered regularly interspaced short palindromic repeats (CRISPRs), prophage sequence profiling, antibiotic resistance profile and plasmid typing methods were less discriminatory and could not confirm the source of the outbreak. Conclusions: Foodborne salmonellosis is an important concern for public health therefore, it is crucial to use accurate, reliable and highly discriminative subtyping methods for epidemiological surveillance and outbreak investigation. In this study, we showed that SNP-based analyses do not only have the ability to confirm the occurrence of the outbreak but also to provide definitive evidence of the source of the outbreak in real-time

Prevalence of Postpartum Family Planning Service Coverage in Selected Referral Facilities of Nepal

Introduction: Nepal Society of Obstetricians and Gynecologists jointly with the Nepalese government and with the support from the International Federation of Obstetrics and Gynecology has implemented an initiative to institutionalize postpartum family planning services in selected major referral facilities of Nepal to address the gap of low uptake of postpartum family planning in Nepal. The aim of the study is to find the prevalence of the service coverage of postpartum contraception in the selected facilities. Methods: A descriptive cross-sectional study was conducted in seven major referral facilities across Nepal. Data were collected from the hospital records of all women who delivered in these facilities between October 2018 and March 2019. Ethical approval for this study was obtained from Nepal Health Research Council. Data analysis was done with SPSS version 23. Results: Among the 29,072 deliveries from all the facilities, postpartum family planning counseling coverage was 27,301 (93.9%). The prevalence of uptake of Postpartum Intrauterine Device is 1581 (5.4%) and female sterilization is 1830 (6.3%). In total 11387 mothers (52.2%) had the intention to choose a postpartum family planning method. However, 36% of mothers neither used nor had the intention to choose a postpartum family planning method. Conclusions: The coverage of Postpartum Intrauterine Device counseling service coverage in Nepal is higher in 2018 as compared to 2016-2017 and in other countries implementing Postpartum Intrauterine Device initiatives. However, the prevalence of service coverage of immediate Postpartum Family Planning methods, mainly Postpartum Intrauterine Device in 2018 is lower in Nepal as compared to 2016-2017, and other countries implementing Postpartum Intrauterine Device initiative. More efforts are needed to encourage mothers delivering in the facilities to use the postpartum family planning method

Discrete Dynamical Systems: A Brief Survey

Dynamical system is a mathematical formalization for any fixed rule that is described in time dependent fashion. The time can be measured by either of the number systems - integers, real numbers, complex numbers. A discrete dynamical system is a dynamical system whose state evolves over a state space in discrete time steps according to a fixed rule. This brief survey paper is concerned with the part of the work done by José Sousa Ramos [2] and some of his research students. We present the general theory of discrete dynamical systems and present results from applications to geometry, graph theory and synchronization

WKB Approximation to the Power Wall

We present a semiclassical analysis of the quantum propagator of a particle confined on one side by a steeply, monotonically rising potential. The models studied in detail have potentials proportional to $x^{\alpha}$ for $x>0$; the limit $\alpha\to\infty$ would reproduce a perfectly reflecting boundary, but at present we concentrate on the cases $\alpha =1$ and 2, for which exact solutions in terms of well known functions are available for comparison. We classify the classical paths in this system by their qualitative nature and calculate the contributions of the various classes to the leading-order semiclassical approximation: For each classical path we find the action $S$, the amplitude function $A$ and the Laplacian of $A$. (The Laplacian is of interest because it gives an estimate of the error in the approximation and is needed for computing higher-order approximations.) The resulting semiclassical propagator can be used to rewrite the exact problem as a Volterra integral equation, whose formal solution by iteration (Neumann series) is a semiclassical, not perturbative, expansion. We thereby test, in the context of a concrete problem, the validity of the two technical hypotheses in a previous proof of the convergence of such a Neumann series in the more abstract setting of an arbitrary smooth potential. Not surprisingly, we find that the hypotheses are violated when caustics develop in the classical dynamics; this opens up the interesting future project of extending the methods to momentum space.Comment: 30 pages, 8 figures. Minor corrections in v.

Counting crocodiles from the sky: Monitoring the critically endangered gharial (Gavialis gangeticus) population with an Unmanned Aerial Vehicle (UAV).

Technology is rapidly changing the methods in the field of wildlife monitoring. Unmanned aerial vehicle (UAV) is an example of a new technology that allows biologists to take to the air to monitor wildlife. Fixed Wing UAV was used to monitor critically endangered gharial population along 46 km of the Babai River in Bardia National Park. The UAV was flown at an altitude of 80 m along 12 pre-designed missions with a search effort of 2.72 hours of flight time acquired a total of 11,799 images covering an effective surface area of 8.2 km2 of river bank habitat. The images taken from the UAV could differentiate between gharial and muggers. A total count of 33 gharials and 31 muggers with observed density (per km2) of 4.64 and 4.0 for gharial and mugger respectively. Comparison of count data between one-time UAV and multiple conventional visual encounter rate surveys data showed no significant difference in the mean. Basking season and turbidity were important factors for monitoring crocodiles along the river bank habitat. Efficacy of monitoring crocodiles by UAV at the given altitude can be replicated in high priority areas with less operating cost and acquisition of high resolution data

Implementation of rapid rule out of myocardial infarction using high-sensitivity troponin : cross-sectional survey of English hospitals

OBJECTIVES: Recent guidance recommended use of high-sensitivity troponin for rapid rule out of myocardial infarction (MI) in the English health service. We aimed to determine the extent of implementation of this guidance across English hospitals. METHODS: This study conducted a cross-sectional questionnaire survey of 131 English acute hospitals with over 10 000 admissions per year. RESULTS: We received 125/131 responses (95%), with 110/125 (88%) reporting use of a high-sensitivity troponin assay and responses showing progressive implementation over the last 10 years. High-sensitivity troponin was reported to be used for rapid rule out of MI in 92/110 Trusts (84%). Review of guidelines received from 95/110 Trusts identified that 71/95 (75%) provided guidance for rapid MI rule out with high-sensitivity troponin: 57 recommended testing at 0 and 3 hours, 4 recommended testing at 0 and 2 hours, and 9 recommended testing at 0 and 1 hour, and timing was unclear at one Trust. CONCLUSIONS: English acute hospital Trusts report widespread implementation of high-sensitivity troponin for rapid rule out of MI, with most recommending testing at 0 and 3 hours

Improving post-partum family planning services provided by female community health volunteers in Nepal: a mixed methods study.

BACKGROUND: Family planning services in the post-partum period, termed post-partum family planning (PPFP) is critical to cover the unmet need for contraception, especially when institutional delivery rates have increased. However, the intention to choose PPFP methods such as post-partum intrauterine devices (PPIUD) remains low in countries such as Nepal. Community health workers such as Female Community Health Volunteers (FCHVs) could play an important role in improving the service coverage of PPFP in Nepal. However, their knowledge of PPFP and community-based services related to PPFP remain unclear. This study aims to assess the effect on community-based PPFP services by improving FCHV's knowledge through orientation on PPFP. METHODS: We conducted this mixed-methods study in Morang District in Nepal. The intervention involved orientation of FCHVs on PPFP methods. We collected quantitative data from three sources; via a survey of FCHVs that assessed their knowledge before and after the intervention, from their monthly reporting forms on counseling coverage of women at different stages of pregnancy from the communities, and by interviewing mothers in their immediate post-partum period in two selected hospitals. We also conducted six focus group discussions with the FCHVs to understand their perception of PPFP and the intervention. We performed descriptive and multivariable analyses for quantitative results and thematic analysis for qualitative data. RESULTS: In total, 230 FCHVs participated in the intervention and their knowledge of PPFP improved significantly after it. The intervention was the only factor significantly associated with their improved knowledge (adjusted odds ratio = 24, P < 0.001) in the multivariable analysis. FCHVs were able to counsel 83.3% of 1872 mothers at different stages of pregnancy in the communities. In the two hospitals, the proportion of mothers in their immediate post-partum period whom reported they were counseled by FCHVs during their pregnancy increased. It improved from 7% before the intervention to 18.1% (P < 0.001) after the intervention. The qualitative findings suggested that the intervention improved their knowledge in providing PPFP counseling. CONCLUSION: The orientation improved the FCHV's knowledge of PPFP and their community-based counseling. Follow-up studies are needed to assess the longer term effect of the FCHV's role in improving community-based PPFP services