scholarly journals Strengthening Surveillance Systems for Malaria Elimination by Integrating Molecular and Genomic Data

2019 ◽  
Vol 4 (4) ◽  
pp. 139 ◽  
Author(s):  
Christian Nsanzabana
Keyword(s):  
Malaria Elimination ◽  
Cost Effective ◽  
Morbidity And Mortality ◽  
Surveillance Systems ◽  
Computing Power ◽  
Routine Surveillance ◽  
Substantial Investment ◽  
Trained Staff ◽  
Polymerase Chain ◽  
Next Generation Sequencing Ngs

Unprecedented efforts in malaria control over the last 15 years have led to a substantial decrease in both morbidity and mortality in most endemic settings. However, these progresses have stalled over recent years, and resurgence may cause dramatic impact on both morbidity and mortality. Nevertheless, elimination efforts are currently going on with the objective of reducing malaria morbidity and mortality by 90% and malaria elimination in at least 35 countries by 2030. Strengthening surveillance systems is of paramount importance to reach those targets, and the integration of molecular and genomic techniques into routine surveillance could substantially improve the quality and robustness of data. Techniques such as polymerase chain reaction (PCR) and quantitative PCR (qPCR) are increasingly available in malaria endemic countries, whereas others such as sequencing are already available in a few laboratories. However, sequencing, especially next-generation sequencing (NGS), requires sophisticated infrastructure with adequate computing power and highly trained personnel for data analysis that require substantial investment. Different techniques will be required for different applications, and cost-effective planning must ensure the appropriate use of available resources. The development of national and sub-regional reference laboratories could help in minimizing the resources required in terms of equipment and trained staff. Concerted efforts from different stakeholders at national, sub-regional, and global level are needed to develop the required framework to establish and maintain these reference laboratories.

scholarly journals Sustainability of a mobile phone application-based data reporting system in Myanmar’s malaria elimination program: a qualitative study

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Win Han Oo ◽  
Kaung Myat Thu ◽  
Julia C. Cutts ◽  
Win Htike ◽  
Kyawt Mon Win ◽  
...  
Keyword(s):  
Mobile Phone ◽  
Mobile Phones ◽  
Malaria Elimination ◽  
User Satisfaction ◽  
Parallel Systems ◽  
Cost Effective ◽  
Surveillance Systems ◽  
Malaria Surveillance ◽  
System Integrity ◽  
Case Based

Abstract Background Strengthening surveillance systems to collect near-real-time case-based data plays a fundamental role in achieving malaria elimination in the Greater Mekong Subregion (GMS). With the advanced and widespread use of digital technology, mHealth is increasingly taking a prominent role in malaria surveillance systems in GMS countries, including Myanmar. In Myanmar’s malaria elimination program, an mHealth system called Malaria Case-based Reporting (MCBR) has been applied for case-based reporting of malaria data by integrated community malaria volunteers (ICMVs). However, the sustainability of such mHealth systems in the context of existing malaria elimination programs in Myanmar is unknown. Methods Focus group discussions were conducted with ICMVs and semi-structured in-depth interviews were conducted with malaria program stakeholders from Myanmar’s Ministry of Health and Sports and its malaria program implementing partners. Thematic (deductive followed by inductive) analysis was undertaken using a qualitative descriptive approach. Results Technological and financial constraints such as inadequate internet access, software errors, and insufficient financial resources to support mobile phone-related costs have hampered users’ access to MCBR. Poor system integrity, unpredictable reporting outcomes, inadequate human resources for system management, and inefficient user support undermined the perceived quality of the system and user satisfaction, and hence its sustainability. Furthermore, multiple parallel systems with functions overlapping those of MCBR were in use. Conclusions Despite its effectiveness and efficiency in malaria surveillance, the sustainability of nationwide implementation of MCBR is uncertain. To make it sustainable, stakeholders should deploy a dedicated human workforce with the necessary technical and technological capacities; secure sustainable, long-term funding for implementation of MCBR; find an alternative cost-effective plan for ensuring sustainable system access by ICMVs, such as using volunteer-owned mobile phones for reporting rather than supporting new mobile phones to them; and find a solution to the burden of multiple parallel systems. Trial registration Not applicable.

Quality Assessment of Hospital Discharge Database for Routine Surveillance of Hip and Knee Arthroplasty–Related Infections

2014 ◽  
Vol 35 (6) ◽  
pp. 646-651 ◽  
Author(s):  
Leslie Grammatico-Guillon ◽  
Sabine Baron ◽  
Christophe Gaborit ◽  
Emmanuel Rusch ◽  
Pascal Astagneau
Keyword(s):  
Hospital Discharge ◽  
Knee Arthroplasty ◽  
Predictive Value ◽  
Surveillance System ◽  
Cost Effective ◽  
International Classification Of Diseases ◽  
Case Definition ◽  
Surveillance Systems ◽  
Routine Surveillance ◽  
Hospital Stays

Objective.Surgical site infection (SSI) surveillance represents a key method of nosocomial infection control programs worldwide. However, most SSI surveillance systems are considered to be poorly cost effective regarding human and economic resources required for data collection and patient follow up. This study aims to assess the efficacy of using hospital discharge databases (HDDs) as a routine surveillance system for detecting hip or knee arthroplasty–related infections (HKAIs).Methods.A case-control study was conducted among patients hospitalized in the Centre region of France between 2008 and 2010. HKAI cases were extracted from the HDD with various algorithms based on the International Classification of Diseases, Tenth Revision, and procedure codes. The control subjects were patients with hip or knee arthroplasty (HKA) without infection selected at random from the HDD during the study period. The gold standard was medical chart review. Sensitivity (Se), specificity (Spe), positive predictive value (PPV), and negative predictive value (NPV) were calculated to evaluate the efficacy of the surveillance system.Results.Among 18,265 hospital stays for HKA, corresponding to 17,388 patients, medical reports were checked for 1,010 hospital stays (989 patients). We identified 530 cases in total (incidence rate, 1% [95% confidence interval (CI), 0.4%–1.6%), and 333 cases were detected by routine surveillance. As compared with 480 controls, Se was 98%, Spe was 71%, PPV was 63%, and NPV was 99%. Using a more specific case definition, based on a sample of 681 hospital stays, Se was 97%, Spe was 95%, PPV was 87%, and NPV was 98%.Conclusions.This study demonstrates the potential of HDD as a tool for routine SSI surveillance after low-risk surgery, under conditions of having an appropriate algorithm for selecting infections.Infect Control Hosp Epidemiol 2014;35(6):646–651

scholarly journals The Role of Adaptive Surveillance as a Core Intervention to Achieve Malaria Elimination

2021 ◽  
Author(s):  
Arantxa Roca-Feltrer ◽  
Ann-Sophie Stratil ◽  
James K. Tibenderana
Keyword(s):  
Malaria Elimination ◽  
Surveillance Systems ◽  
National Programmes ◽  
Level Increase ◽  
Substantial Investment ◽  
Multi Level ◽  
Link Data ◽  
Operational Guidance ◽  
Case Based

Adaptive surveillance systems are essential for national programmes to achieve their malaria elimination goals. Core principles of surveillance systems including accurate diagnosis and reporting of malaria cases, integration of health data across administrative levels and the need to link data to a response are well defined by international guidelines. Nevertheless, while the requirements of surveillance systems along the transmission continuum are clearly documented, the operationalization remains challenging for national programmes. Firstly, because the multi-level increase of surveillance efforts demanding real-time and case-based data as well as the capacity of the health force to trigger locally customized responses, is resource intensive and requires substantial investment. Secondly, because there is a gap in international alignment on best tools and practices on how to operationally implement these requirements. Recently, several initiatives have started to address this gap in international coordination, aiming to establish the operational guidance for elimination programmes to successfully implement adaptive surveillance systems.

scholarly journals Sustainability of a Mobile Phone Application-Based Data Reporting System in Myanmar’s Malaria Elimination Program: A Qualitative Study

2021 ◽  
Author(s):  
Win Han Oo ◽  
Kaung Myat Thu ◽  
Julia Cutts ◽  
Win Htike ◽  
Kyawt Mon Win ◽  
...  
Keyword(s):  
Mobile Phone ◽  
Mobile Phones ◽  
Malaria Elimination ◽  
User Satisfaction ◽  
Parallel Systems ◽  
Cost Effective ◽  
Surveillance Systems ◽  
Malaria Surveillance ◽  
System Integrity ◽  
Case Based

Abstract Background Strengthening surveillance systems to collect near-real-time case-based data plays a fundamental role in achieving malaria elimination in the Greater Mekong Subregion (GMS). With the advanced and widespread use of digital technology, mHealth is increasingly taking a prominent role in malaria surveillance systems in GMS countries, including Myanmar. In Myanmar’s malaria elimination program, an mHealth system called Malaria Case-based Reporting (MCBR) has been applied for case-based reporting of malaria data by integrated community malaria volunteers (ICMVs). However, the sustainability of such mHealth systems in the context of existing malaria elimination programs in Myanmar is unknown. Methods Focus group discussions were conducted with ICMVs and semi-structured in-depth interviews were conducted with malaria program stakeholders from Myanmar’s Ministry of Health and Sports and its malaria program implementing partners. Thematic (deductive followed by inductive) analysis was undertaken using a qualitative descriptive approach. Results Technological and financial constraints such as inadequate internet access, software errors, and insufficient financial resources to support mobile phone-related costs have hampered users’ access to MCBR. Poor system integrity, unpredictable reporting outcomes, inadequate human resources for system management, and inefficient user support undermined the perceived quality of the system and user satisfaction, and hence its sustainability. Furthermore, multiple parallel systems with functions overlapping those of MCBR were in use. Conclusions Despite its effectiveness and efficiency in malaria surveillance, the sustainability of nationwide implementation of MCBR is uncertain. To make it sustainable, stakeholders should deploy a dedicated human workforce with the necessary technical and technological capacities; secure sustainable, long-term funding for implementation of MCBR; find an alternative cost-effective plan for ensuring sustainable system access by ICMVs, such as using volunteer-owned mobile phones for reporting rather than supporting new mobile phones to them; and find a solution to the burden of multiple parallel systems. Trial registration: Not applicable

Malaria elimination in India requires additional surveillance mechanisms

2021 ◽  
Author(s):  
Manju Rahi ◽  
Payal Das ◽  
Amit Sharma
Keyword(s):  
Real Time ◽  
Malaria Elimination ◽  
Surveillance Data ◽  
Surveillance Systems ◽  
Malaria Surveillance ◽  
Aggregated Data ◽  
Malaria Burden ◽  
The Core ◽  
Reporting Systems ◽  
Geographic Regions

Abstract Malaria surveillance is weak in high malaria burden countries. Surveillance is considered as one of the core interventions for malaria elimination. Impressive reductions in malaria-associated morbidity and mortality have been achieved across the globe, but sustained efforts need to be bolstered up to achieve malaria elimination in endemic countries like India. Poor surveillance data become a hindrance in assessing the progress achieved towards malaria elimination and in channelizing focused interventions to the hotspots. A major obstacle in strengthening India’s reporting systems is that the surveillance data are captured in a fragmented manner by multiple players, in silos, and is distributed across geographic regions. In addition, the data are not reported in near real-time. Furthermore, multiplicity of malaria data resources limits interoperability between them. Here, we deliberate on the acute need of updating India’s surveillance systems from the use of aggregated data to near real-time case-based surveillance. This will help in identifying the drivers of malaria transmission in any locale and therefore will facilitate formulation of appropriate interventional responses rapidly.

scholarly journals Structural Mapping of Mutations in Spike, RdRp and Orf3a Genes of SARS-CoV-2 in Influenza Like Illness (ILI) Patients

Viruses ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 136
Author(s):  
Bandar Alosaimi ◽  
Asif Naeem ◽  
Majed F. Alghoribi ◽  
Lilian Okdah ◽  
Maaweya E. Hamed ◽  
...  
Keyword(s):  
Surveillance Systems ◽  
Case Definitions ◽  
Structural Mapping ◽  
Policy Makers ◽  
Influenza Like Illness ◽  
Spike Gene ◽  
Ambulatory Patients ◽  
Community Transmission ◽  
Next Generation Sequencing Ngs ◽  
Epidemiological Link

In December 2019, the emergence of SARS-CoV-2 virus in China led to a pandemic. Since both Influenza Like Illness (ILI) and COVID-19 case definitions overlap, we re-investigated the ILI cases using PCR for the presence of SARS-CoV-2 in 739 nasopharyngeal swabs collected from November 2019 to March 2020. SARS-CoV-2 RNA was found in 37 samples (5%) collected mostly during February 2020. It was followed by confirmation of evolutionary and spatial relationships using next generation sequencing (NGS). We observed that the overall incidence of ILI cases during 2019–2020 influenza season was considerably higher than previous years and was gradually replaced with SARS-CoV-2, which indicated a silent transmission among ambulatory patients. Sequencing of representative isolates confirmed independent introductions and silent transmission earlier than previously thought. Evolutionary and spatial analyses revealed clustering in the GH clade, characterized by three amino acid substitutions in spike gene (D614G), RdRp (P323L) and NS3 (Q57H). P323L causes conformational change near nsp8 binding site that might affect virus replication and transcription. In conclusion, assessment of the community transmission among patients with mild COVID-19 illness, particularly those without epidemiological link for acquiring the virus, is of utmost importance to guide policy makers to optimize public health interventions. The detection of SARS-CoV-2 in ILI cases shows the importance of ILI surveillance systems and warrants its further strengthening to mitigate the ongoing transmission of SARS-CoV-2. The effect of NS3 substitutions on oligomerization or membrane channel function (intra- and extracellular) needs functional validation.

Cost-Effectiveness of Nasopharyngeal Carcinoma Screening with Epstein-Barr Virus Polymerase Chain Reaction or Serology in High-Incidence Populations Worldwide

2020 ◽  
Author(s):  
Jacob A Miller ◽  
Quynh-Thu Le ◽  
Benjamin A Pinsky ◽  
Hannah Wang
Keyword(s):  
Cost Effectiveness ◽  
Epstein Barr Virus ◽  
Cost Effective ◽  
Chain Reaction ◽  
Men And Women ◽  
Barr Virus ◽  
Screening Strategies ◽  
High Incidence ◽  
Polymerase Chain ◽  
Epstein Barr

Abstract Background The incidence of endemic Epstein-Barr Virus (EBV)-associated nasopharyngeal carcinoma (NPC) varies considerably worldwide. In high-incidence regions, screening trials have been conducted. We estimated the mortality reduction and cost-effectiveness of EBV-based NPC screening in populations worldwide. Methods We identified 380 populations in 132 countries with incident NPC and developed a decision-analytic model to compare ten unique onetime screening strategies to no screening for men and women at age 50 years. Screening performance and the stage distribution of undiagnosed NPC were derived from a systematic review of prospective screening trials. Results Screening was cost-effective in up to 14.5% of populations, depending on the screening strategy. These populations were limited to East Asia, Southeast Asia, North Africa, or were Asian, Pacific Islander, or Inuit populations in North America. A combination of serology and nasopharyngeal polymerase chain reaction (PCR) was most cost-effective, but other combinations of serologic and/or plasma PCR screening were also cost-effective. The estimated reduction in NPC mortality was similar across screening strategies. For a hypothetical cohort of patients in China, 10-year survival improved from 71.0% (95%CI = 68.8%–73.0%) without screening to a median of 86.3% (range = 83.5%–88.2%) with screening. This corresponded to a median 10-year reduction in NPC mortality of 52.9% (range= 43.1%–59.3%). Screening interval impacted absolute mortality reduction and cost-effectiveness. Conclusions We observed decreased NPC mortality with EBV-based screening. Screening was cost-effective in many high-incidence populations and could be extended to men and women as early as age 40 years in select regions. These findings may be useful when choosing among local public health initiatives.

scholarly journals Evaluation of Ion Torrent next-generation sequencing for thalassemia diagnosis

2020 ◽  
Vol 48 (12) ◽  
pp. 030006052096777
Author(s):  
Peisong Chen ◽  
Xuegao Yu ◽  
Hao Huang ◽  
Wentao Zeng ◽  
Xiaohong He ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Ion Torrent ◽  
Next Generation ◽  
Large Deletions ◽  
Different Types ◽  
Variant Detection ◽  
Polymerase Chain ◽  
Next Generation Sequencing Ngs ◽  
Accuracy And Repeatability ◽  
Generation Sequencing

Introduction To evaluate a next-generation sequencing (NGS) workflow in the screening and diagnosis of thalassemia. Methods In this prospective study, blood samples were obtained from people undergoing genetic screening for thalassemia at our centre in Guangzhou, China. Genomic DNA was polymerase chain reaction (PCR)-amplified and sequenced using the Ion Torrent system and results compared with traditional genetic analyses. Results Of the 359 subjects, 148 (41%) were confirmed to have thalassemia. Variant detection identified 35 different types including the most common. Identification of the mutational sites by NGS were consistent with those identified by Sanger sequencing and Gap-PCR. The sensitivity and specificities of the Ion Torrent NGS were 100%. In a separate test of 16 samples, results were consistent when repeated ten times. Conclusion Our NGS workflow based on the Ion Torrent sequencer was successful in the detection of large deletions and non-deletional defects in thalassemia with high accuracy and repeatability.

scholarly journals 781. C.difficile PCR+/ Toxin EIA- treat or not treat? A clinician survey

2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S435-S436
Author(s):  
Sarath G Nath ◽  
Francesca Lee ◽  
Anjali Bararia ◽  
Ank E Nijhawan
Keyword(s):  
Clinical Judgment ◽  
Clinical Care ◽  
Cost Effective ◽  
False Positive Diagnosis ◽  
Missed Diagnosis ◽  
Stool Samples ◽  
Polymerase Chain ◽  
Low Sensitivity ◽  
Survey Responses ◽  
And Training

Abstract Background C.difficile Toxin Polymerase Chain Reaction (C.diff PCR) and C.difficile Toxin Enzyme Immunoassays (toxin EIA) are commonly used tests to diagnose Clostridoides difficile infection (CDI). C.diff PCR cannot differentiate between colonization and infection, leading to a higher false-positive diagnosis of CDI. Toxin EIA has low sensitivity leading to a missed diagnosis of CDI. In patients with C.diff PCR positive(+) and Toxin EIA negative(-), clinical judgment is often needed regarding the decision to treat or not to treat. C.diff cytotoxic assay (CCA), is a more sensitive method to detect the toxin but is time-consuming and not readily available. Methods Between 6/2019 and 12/2019, 83 patients who were admitted to the hospital, met our inclusion criteria (C.diff PCR+/EIA-). Clinicians who cared for these patients were contacted and surveyed with a predesigned questionnaire evaluating the rationale of treatment. Also, a simultaneous medical records review was done to ensure consistency. Along with this C.diff PCR+/EIA- stool samples were sent to ARUP laboratories for CCA. The CCA results were not available for clinicians and did not impact clinical care. Average cost for a CCA assay was $29 Results Demographics of the clinicians were variable (Table 1). Several parameters were considered when making decisions regarding treatment and GI/ID were frequently involved (figure 1). Among the 83 patients, 41(49%) were CCA (+) and 42(51%) were CCA (-). 48 of 83 (58%) patients received treatment for CDI. 25 of 48 (52%) patients who were treated were CCA positive while 23 of 48 (48%) patients were CCA negative. Among the untreated patients, 16/35 (46%) were CCA+ while 19/35(54%) were CCA-. There was no statistically significant correlation between clinical judgment and CCA assay results (p: 0.56 on the Chi test). Demographics of the clinicians Clinician survey responses CDI Treatment and by CCA positivity Conclusion Clinicians regardless of their background and training face challenges with the treatment of C.diff PCR+/EIA- patients. Patient outcomes based on the incorporation of CCA assay into an algorithm for C.diff PCR+/EIA- patients, need to be evaluated. But it has a potential role in stopping unnecessary CDI treatment as well as avoidance of missed treatment opportunities while possibly also being cost-effective. Disclosures Ank E. Nijhawan, MD, MPH, Gilead (Grant/Research Support, Scientific Research Study Investigator, Research Grant or Support)

scholarly journals The effect of silica desiccation under different storage conditions on filter-immobilized environmental DNA

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Michael J. Allison ◽  
Jessica M. Round ◽  
Lauren C. Bergman ◽  
Ali Mirabzadeh ◽  
Heather Allen ◽  
...  
Keyword(s):  
Silica Gel ◽  
Storage Temperature ◽  
Environmental Dna ◽  
Cost Effective ◽  
Storage Conditions ◽  
Systematic Evaluation ◽  
Silica Bead ◽  
Gel Beads ◽  
Polymerase Chain

Abstract Objective Silica gel beads have promise as a non-toxic, cost-effective, portable method for storing environmental DNA (eDNA) immobilized on filter membranes. Consequently, many ecological surveys are turning to silica bead filter desiccation rather than ethanol preservation. However, no systematic evaluation of silica bead storage conditions or duration past 1 week has been published. The present study evaluates the quality of filter-immobilized eDNA desiccated with silica gel under different storage conditions for over a year using targeted quantitative real-time polymerase chain reaction (qPCR)-based assays. Results While the detection of relatively abundant eDNA target was stable over 15 months from either ethanol- or silica gel-preserved filters at − 20 and 4 °C, silica gel out-performed ethanol preservation at 23 °C by preventing a progressive decrease in eDNA sample quality. Silica gel filter desiccation preserved low abundance eDNA equally well up to 1 month regardless of storage temperature (18, 4, or − 20 °C). However only storage at − 20 °C prevented a noticeable decrease in detectability at 5 and 12 months. The results indicate that brief storage of eDNA filters with silica gel beads up to 1 month can be successfully accomplished at a range of temperatures. However, longer-term storage should be at − 20 °C to maximize sample integrity.

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