scholarly journals Development and Implementation of Multiplex TaqMan Array Cards for Specimen Testing at Child Health and Mortality Prevention Surveillance Site Laboratories

2019 ◽  
Vol 69 (Supplement_4) ◽  
pp. S311-S321 ◽  
Author(s):  
Maureen H Diaz ◽  
Jessica L Waller ◽  
M Jordan Theodore ◽  
Nishi Patel ◽  
Bernard J Wolff ◽  
...  
Keyword(s):  
Child Health ◽  
Data Management ◽  
Real Time ◽  
Sub Saharan Africa ◽  
Quality Data ◽  
Molecular Testing ◽  
Acid Extraction ◽  
Infectious Disease Diagnostics ◽  
Taqman Array ◽  
Health And Mortality

Abstract Child Health and Mortality Prevention Surveillance (CHAMPS) laboratories are employing a variety of laboratory methods to identify infectious agents contributing to deaths of children <5 years old and stillbirths in sub-Saharan Africa and South Asia. In support of this long-term objective, our team developed TaqMan Array Cards (TACs) for testing postmortem specimens (blood, cerebrospinal fluid, lung tissue, respiratory tract swabs, and rectal swabs) for >100 real-time polymerase chain reaction (PCR) targets in total (30–45 per card depending on configuration). Multipathogen panels were configured by syndrome and customized to include pathogens of significance in young children within the regions where CHAMPS is conducted, including bacteria (57 targets covering 30 genera), viruses (48 targets covering 40 viruses), parasites (8 targets covering 8 organisms), and fungi (3 targets covering 3 organisms). The development and application of multiplex real-time PCR reactions to the TAC microfluidic platform increased the number of targets in each panel while maintaining assay efficiency and replicates for heightened sensitivity. These advances represent a substantial improvement in the utility of this technology for infectious disease diagnostics and surveillance. We optimized all aspects of the CHAMPS molecular laboratory testing workflow including nucleic acid extraction, quality assurance, and data management to ensure comprehensive molecular testing of specimens and high-quality data. Here we describe the development and implementation of multiplex TACs and associated laboratory protocols for specimen processing, testing, and data management at CHAMPS site laboratories.

scholarly journals Mortality Surveillance Methods to Identify and Characterize Deaths in Child Health and Mortality Prevention Surveillance Network Sites

2019 ◽  
Vol 69 (Supplement_4) ◽  
pp. S262-S273 ◽  
Author(s):  
Navit T Salzberg ◽  
Kasthuri Sivalogan ◽  
Quique Bassat ◽  
Allan W Taylor ◽  
Sunday Adedini ◽  
...  
Keyword(s):  
Child Health ◽  
South Asia ◽  
Cause Of Death ◽  
Demographic Data ◽  
Childhood Mortality ◽  
Sub Saharan Africa ◽  
Quality Data ◽  
Sub Saharan ◽  
Mortality Surveillance ◽  
Health And Mortality

Abstract Despite reductions over the past 2 decades, childhood mortality remains high in low- and middle-income countries in sub-Saharan Africa and South Asia. In these settings, children often die at home, without contact with the health system, and are neither accounted for, nor attributed with a cause of death. In addition, when cause of death determinations occur, they often use nonspecific methods. Consequently, findings from models currently utilized to build national and global estimates of causes of death are associated with substantial uncertainty. Higher-quality data would enable stakeholders to effectively target interventions for the leading causes of childhood mortality, a critical component to achieving the Sustainable Development Goals by eliminating preventable perinatal and childhood deaths. The Child Health and Mortality Prevention Surveillance (CHAMPS) Network tracks the causes of under-5 mortality and stillbirths at sites in sub-Saharan Africa and South Asia through comprehensive mortality surveillance, utilizing minimally invasive tissue sampling (MITS), postmortem laboratory and pathology testing, verbal autopsy, and clinical and demographic data. CHAMPS sites have established facility- and community-based mortality notification systems, which aim to report potentially eligible deaths, defined as under-5 deaths and stillbirths within a defined catchment area, within 24–36 hours so that MITS can be conducted quickly after death. Where MITS has been conducted, a final cause of death is determined by an expert review panel. Data on cause of death will be provided to local, national, and global stakeholders to inform strategies to reduce perinatal and childhood mortality in sub-Saharan Africa and South Asia.

Impact of Data Quality on Well Operations: Case Study of Work-over Operations

2016 ◽  
Author(s):  
Alfred Enyekwe ◽  
Osahon Urubusi ◽  
Raufu Yekini ◽  
Iorkam Azoom ◽  
Oloruntoba Isehunwa
Keyword(s):  
Data Quality ◽  
Data Management ◽  
Real Time ◽  
Data Management System ◽  
Quality Data ◽  
Process Safety ◽  
Well Control ◽  
Drilling Operations ◽  
Short Time

ABSTRACT Significant emphasis on data quality is placed on real-time drilling data for the optimization of drilling operations and on logging data for quality lithological and petrophysical description of a field. This is evidenced by huge sums spent on real time MWD/LWD tools, broadband services, wireline logging tools, etc. However, a lot more needs to be done to harness quality data for future workover and or abandonment operations where data being relied on is data that must have been entered decades ago and costs and time spent are critically linked to already known and certified information. In some cases, data relied on has been migrated across different data management platforms, during which relevant data might have been lost, mis-interpreted or mis-placed. Another common cause of wrong data is improperly documented well intervention operations which have been done in such a short time, that there is no pressure to document the operation properly. This leads to confusion over simple issues such as what depth a plug was set, or what junk was left in hole. The relative lack of emphasis on this type of data quality has led to high costs of workover and abandonment operations. In some cases, well control incidents and process safety incidents have arisen. This paper looks at over 20 workover operations carried out in a span of 10 years. An analysis is done on the wells’ original timeline of operation. The data management system is generally analyzed and a categorization of issues experienced during the workover operations is outlined. Bottlenecks in data management are defined and solutions currently being implemented to manage these problems are listed as recommended good practices.

scholarly journals Pathology and Telepathology Methods in the Child Health and Mortality Prevention Surveillance Network

2019 ◽  
Vol 69 (Supplement_4) ◽  
pp. S322-S332 ◽  
Author(s):  
Roosecelis B Martines ◽  
Jana M Ritter ◽  
Joy Gary ◽  
Wun-Ju Shieh ◽  
Jaume Ordi ◽  
...  
Keyword(s):  
Child Health ◽  
Lessons Learned ◽  
Molecular Testing ◽  
Surveillance Network ◽  
Pathology Laboratory ◽  
Pathologic Evaluation ◽  
Control And Prevention ◽  
Central Pathology ◽  
Image Archives ◽  
Health And Mortality

Abstract This manuscript describes the Child Health and Mortality Prevention Surveillance (CHAMPS) network approach to pathologic evaluation of minimally invasive tissue sampling (MITS) specimens, including guidelines for histopathologic examination and further diagnostics with special stains, immunohistochemistry, and molecular testing, as performed at the CHAMPS Central Pathology Laboratory (CPL) at the Centers for Disease Control and Prevention, as well as techniques for virtual discussion of these cases (telepathology) with CHAMPS surveillance locations. Based on review of MITS from the early phase of CHAMPS, the CPL has developed standardized histopathology-based algorithms for achieving diagnoses from MITS and telepathology procedures in conjunction with the CHAMPS sites, with the use of whole slide scanners and digital image archives, for maximizing concurrence and knowledge sharing between site and CPL pathologists. These algorithms and procedures, along with lessons learned from initial implementation of these approaches, guide pathologists at the CPL and CHAMPS sites through standardized diagnostics of MITS cases, and allow for productive, real-time case discussions and consultations.

scholarly journals Setting up child health and mortality prevention surveillance in Ethiopia

2021 ◽  
Vol 5 ◽  
pp. 173
Author(s):  
Anna C. Seale ◽  
Nega Assefa ◽  
Lola Madrid ◽  
Stefanie Wittmann ◽  
Hanan Abdurahman ◽  
...  
Keyword(s):  
Child Health ◽  
Cause Of Death ◽  
High Mortality ◽  
Demographic Data ◽  
Child Death ◽  
Sub Saharan Africa ◽  
London School ◽  
Eastern Ethiopia ◽  
Live Births ◽  
Health And Mortality

Background: Mortality rates for children under five years of age, and stillbirth risks, remain high in parts of sub-Saharan Africa and South Asia. The Child Health and Mortality Prevention Surveillance (CHAMPS) network aims to ascertain causes of child death in high child mortality settings (>50 deaths/1000 live-births). We aimed to develop a “greenfield” site for CHAMPS, based in Harar and Kersa, in Eastern Ethiopia. This very high mortality setting (>100 deaths/1000 live-births in Kersa) had limited previous surveillance capacity, weak infrastructure and political instability. Here we describe site development, from conception in 2015 to the end of the first year of recruitment. Methods: We formed a collaboration between Haramaya University and the London School of Hygiene & Tropical Medicine and engaged community, national and international partners to support a new CHAMPS programme. We developed laboratory infrastructure and recruited and trained staff. We established project specific procedures to implement CHAMPS network protocols including; death notifications, clinical and demographic data collection, post-mortem minimally invasive tissue sampling, microbiology and pathology testing, and verbal autopsy. We convened an expert local panel to determine cause-of-death. In partnership with the Ethiopian Public Health Institute we developed strategies to improve child and maternal health. Results: Despite considerable challenge, with financial support, personal commitment and effective partnership, we successfully initiated CHAMPS. One year into recruitment (February 2020), we had received 1173 unique death notifications, investigated 59/99 MITS-eligible cases within the demographic surveillance site, and assigned an underlying and immediate cause of death to 53 children. Conclusions: The most valuable data for global health policy are from high mortality settings, but initiating CHAMPS has required considerable resource. To further leverage this investment, we need strong local research capacity and to broaden the scientific remit. To support this, we have set up a new collaboration, the “Hararghe Health Research Partnership”.

Research Data Management Among Researchers in Higher Learning Institutions of Sub-Saharan Africa

2020 ◽  
pp. 479-488 ◽  
Author(s):  
Neema Florence Mosha ◽  
Edith Talina Luhanga ◽  
Mary Vincent Mosha ◽  
Janeth Jonathan Marwa
Keyword(s):  
Data Management ◽  
Information And Communication Technologies ◽  
Management Plan ◽  
Research Data ◽  
Sub Saharan Africa ◽  
Quality Data ◽  
Research Data Management ◽  
Information And Communication ◽  
Sub Saharan ◽  
Learning Institutions

Advancement in information and communication technologies has made it easier for researchers to capture and store myriad data at a higher level of granularity. Higher education institutions (HEIs) worldwide are incorporating research data management (RDM) services to enable researchers to work with their data properly. This chapter focuses on creating awareness amongst researchers on how researchers and HEIs can form strategies, design and restrict data management plan (DMP), integrate research data life cycle, and ensure quality data sharing, as well as integrate with developed RDM policies and guidelines to curb challenges prohibiting the practice of RDM in HEIs.

scholarly journals Accuracy of Curable Sexually Transmitted Infections and Genital Mycoplasmas Screening by Multiplex Real-Time PCR Using a Self-Collected Veil among Adult Women in Sub-Saharan Africa

2019 ◽  
Vol 2019 ◽  
pp. 1-15
Author(s):  
Zita Aleyo Nodjikouambaye ◽  
Fabrice Compain ◽  
Damtheou Sadjoli ◽  
Ralph-Sydney Mboumba Bouassa ◽  
Hélène Péré ◽  
...  
Keyword(s):  
Sexually Transmitted Infections ◽  
Real Time ◽  
Real Time Pcr ◽  
Sub Saharan Africa ◽  
Molecular Testing ◽  
Adult Women ◽  
Sampling Device ◽  
Sexually Transmitted ◽  
Sub Saharan ◽  
Genital Mycoplasmas

Background. Sexually transmitted infections (STIs) are highly prevalent in sub-Saharan Africa. Genital self-sampling may facilitate the screening of STIs in hard-to-reach remote populations far from large health care centers and may increase screening rates. The cross-sectional GYNAUTO-STI study was carried out to assess the performance of a novel genital veil (V-Veil-Up Gyn Collection Device, V-Veil-Up Pharma, Ltd., Nicosia, Cyprus) as a genital self-sampling device to collect genital secretions to diagnose STIs by molecular biology as compared to reference clinician-collected genital specimens, in adult African women. Methods. Adult women living in N’Djamena, the capital city of Chad, were recruited from the community and referred to the clinic for women’s sexual health “La Renaissance Plus”. A clinician obtained an endocervical specimen using flocked swab. Genital secretions were also obtained by self-collection using veil. Both clinician- and self-collected specimens were tested for common curable STIs (including Chlamydia trachomatis, Neisseria gonorrhoeae, Mycoplasma genitalium, and Trichomonas vaginalis) and genital Mycoplasma spp. by multiplex real-time PCR (Allplex™ STI Essential Assay, Seegene, Seoul, South Korea). Test positivities for both collection methods were compared by assessing methods agreement, sensitivity, and specificity. Results. A total of 251 women (mean age, 35.1 years) were prospectively enrolled. Only seven (2.8%) women were found to be infected with at least one common STIs [C. trachomatis: 3 (1.2%), N. gonorrhoeae: 1 (0.4%), M. genitalium: 4 (1.6%) and T. vaginalis: 1 (0.4%)], while the prevalence of genital mycoplasmas was much higher (54.2%) with a predominance of Ureaplasma parvum (42.6%). Self-collection by veil was non-inferior to clinician-based collection for genital microorganisms DNA molecular testing, with “almost perfect” agreement between both methods, high sensitivity (97.0%; 95%CI: 92.5-99.2%), and specificity (88.0%; 95%CI: 80.7-93.3%). Remarkably, the mean total number of genital microorganisms detected per woman was 1.14-fold higher in self-collected specimens compared to that in clinician-collected specimens. Conclusions. Veil-based self-collection of female genital secretions constitutes a convenient tool to collect in gentle way cervicovaginal secretions for accurate molecular detection of genital bacteria. Such sampling procedure could be easily implemented in STIs clinics in sub-Saharan Africa.

scholarly journals Overview and Development of the Child Health and Mortality Prevention Surveillance Determination of Cause of Death (DeCoDe) Process and DeCoDe Diagnosis Standards

2019 ◽  
Vol 69 (Supplement_4) ◽  
pp. S333-S341 ◽  
Author(s):  
Dianna M Blau ◽  
J Patrick Caneer ◽  
Rebecca P Philipsborn ◽  
Shabir A Madhi ◽  
Quique Bassat ◽  
...  
Keyword(s):  
Child Health ◽  
Cause Of Death ◽  
Sub Saharan Africa ◽  
World Health ◽  
Mortality Data ◽  
Sequence Of Events ◽  
Decode Process ◽  
Clinical Records ◽  
Health And Mortality

Abstract Mortality surveillance and cause of death data are instrumental in improving health, identifying diseases and conditions that cause a high burden of preventable deaths, and allocating resources to prevent these deaths. The Child Health and Mortality Prevention Surveillance (CHAMPS) network uses a standardized process to define, assign, and code causes of stillbirth and child death (<5 years of age) across the CHAMPS network. A Determination of Cause of Death (DeCoDe) panel composed of experts from a local CHAMPS site analyzes all available individual information, including laboratory, histopathology, abstracted clinical records, and verbal autopsy findings for each case and, if applicable, also for the mother. Using this information, the site panel ascertains the underlying cause (event that precipitated the fatal sequence of events) and other antecedent, immediate, and maternal causes of death in accordance with the International Classification of Diseases, Tenth Revision and the World Health Organization death certificate. Development and use of the CHAMPS diagnosis standards—a framework of required evidence to support cause of death determination—assures a homogenized procedure leading to a more consistent interpretation of complex data across the CHAMPS network. This and other standardizations ensures future comparability with other sources of mortality data produced externally to this project. Early lessons learned from implementation of DeCoDe in 5 CHAMPS sites in sub-Saharan Africa and Bangladesh have been incorporated into the DeCoDe process, and the implementation of DeCoDe has the potential to spur health systems improvements and local public health action.

scholarly journals Building a Centre of Excellence in Data Management in East Africa

2021 ◽  
Author(s):  
Betty Agwang ◽  
Yuka Manabe
Keyword(s):  
Data Collection ◽  
Infectious Diseases ◽  
Clinical Research ◽  
Data Management ◽  
The United States ◽  
Sub Saharan Africa ◽  
Research Quality ◽  
Data Management System ◽  
Quality Data ◽  
High Quality

Abstract Background: In resource-limited settings, there is a paucity of high quality data management systems for clinical research. The result is that data are often managed in high-income countries disadvantaging researchers at sites where the data are collected. An institutional data management system to address the data collection concerns of the collaborators and sponsors is a key institutional capacity element for high quality research. Our goal was to build a local data management center to streamline data collection and validation compliant with international regulatory bodies. Methods: Leveraging established collaborations between Office of Cyber Infrastructure and Computational Biology of the National Institutes of Health and the John Hopkins University School of Medicine in the United States, the Infectious Diseases Institute at Makerere University built a data management coordinating center. This included mentorship from the NIAID International Centers for Excellence in Research and training of key personnel in South Africa at a functioning data center. The number of studies, case report forms processed and the number of publications emanating from studies using the data management unit since its inception were tabulated. Results: The Infectious Diseases Institute data management core began processing data in 2009 with 3 personnel, hardware (network-enabled scanners, desktops, server held in Bethesda with nightly back up) and software licenses, in addition to on-site support from the NIH. In the last 10 years, 850,869 pages of data have been processed from 60 studies in Uganda, across sub-Saharan Africa, Asia and South America. Real-time data cleaning and data analysis occur routinely and enhance clinical research quality; a total of 212 publications from IDI investigators have been published over the past 10 years. Apart from the server back-up services provided by the NIH, the center is now self-sustaining from fees charged to individual studies. Conclusion: Collaborative partnership among research institutions enabled the IDI to build a core data management and coordination center to support clinical studies, build institutional research capacity, and to advance data quality and integrity for the investigators and sponsors.

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