Dataset Information

Metagenomic Pathogen Sequencing in Resource-Scarce Settings: Lessons Learned and the Road Ahead.

ABSTRACT: Metagenomic next-generation sequencing (mNGS) is the process of sequencing all genetic material in a biological sample. The technique is growing in popularity with myriad applications including outbreak investigation, biosurveillance, and pathogen detection in clinical samples. However, mNGS programs are costly to build and maintain, and additional obstacles faced by low- and middle-income countries (LMICs) may further widen global inequities in mNGS capacity. Over the past two decades, several important infectious disease outbreaks have highlighted the importance of establishing widespread sequencing capacity to support rapid disease detection and containment at the source. Using lessons learned from the COVID-19 pandemic, LMICs can leverage current momentum to design and build sustainable mNGS programs, which would form part of a global surveillance network crucial to the elimination of infectious diseases.

SUBMITTER: Yek C

PROVIDER: S-EPMC9558322 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Metagenomic Pathogen Sequencing in Resource-Scarce Settings: Lessons Learned and the Road Ahead.

Yek Christina C Pacheco Andrea R AR Vanaerschot Manu M Bohl Jennifer A JA Fahsbender Elizabeth E Aranda-Díaz Andrés A Lay Sreyngim S Chea Sophana S Oum Meng Heng MH Lon Chanthap C Tato Cristina M CM Manning Jessica E JE

Frontiers in epidemiology 20220815

Metagenomic next-generation sequencing (mNGS) is the process of sequencing all genetic material in a biological sample. The technique is growing in popularity with myriad applications including outbreak investigation, biosurveillance, and pathogen detection in clinical samples. However, mNGS programs are costly to build and maintain, and additional obstacles faced by low- and middle-income countries (LMICs) may further widen global inequities in mNGS capacity. Over the past two decades, several ...[more]

PMID: 36247976

Similar Datasets

Project description:BACKGROUND:To develop effective and sustainable simulation training programs in low-resource settings, it is critical that facilitators are thoroughly trained in debriefing, a critical component of simulation learning. However, large knowledge gaps exist regarding the best way to train and evaluate debrief facilitators in low-resource settings. METHODS:Using a mixed methods approach, this study explored the feasibility of evaluating the debriefing skills of nurse mentors in Bihar, India. Videos of obstetric and neonatal post-simulation debriefs were assessed using two known tools: the Center for Advanced Pediatric and Perinatal Education (CAPE) tool and Debriefing Assessment for Simulation in Healthcare (DASH). Video data was used to evaluate interrater reliability and changes in debriefing performance over time. Additionally, twenty semi-structured interviews with nurse mentors explored perceived barriers and enablers of debriefing in Bihar. RESULTS:A total of 73 debriefing videos, averaging 18?min each, were analyzed by two raters. The CAPE tool demonstrated higher interrater reliability than the DASH; 13 of 16 CAPE indicators and two of six DASH indicators were judged reliable (ICC >?0.6 or kappa >?0.40). All indicators remained stable or improved over time. The number of 'instructors questions,' the amount of 'trainee responses,' and the ability to 'organize the debrief' improved significantly over time (p?<?0.01, p?<?0.01, p?=?0.04). Barriers included fear of making mistakes, time constraints, and technical challenges. Enablers included creating a safe learning environment, using contextually appropriate debriefing strategies, and team building. Overall, nurse mentors believed that debriefing was a vital aspect of simulation-based training. CONCLUSION:Simulation debriefing and evaluation was feasible among nurse mentors in Bihar. Results demonstrated that the CAPE demonstrated higher interrater reliability than the DASH and that nurse mentors were able to maintain or improve their debriefing skills overtime. Further, debriefing was considered to be critical to the success of the simulation training. However, fear of making mistakes and logistical challenges must be addressed to maximize learning. Teamwork, adaptability, and building a safe learning environment enhanced the quality enhanced the quality of simulation-based training, which could ultimately help to improve maternal and neonatal health outcomes in Bihar.

Project description:The COVID-19 pandemic highlighted the importance of global genomic surveillance to monitor the emergence and spread of SARS-CoV-2 variants and inform public health decision-making. Until December 2020 there was minimal capacity for viral genomic surveillance in most Caribbean countries. To overcome this constraint, the COVID-19: Infectious disease Molecular epidemiology for PAthogen Control & Tracking (COVID-19 IMPACT) project was implemented to establish rapid SARS-CoV-2 whole genome nanopore sequencing at The University of the West Indies (UWI) in Trinidad and Tobago (T&T) and provide needed SARS-CoV-2 sequencing services for T&T and other Caribbean Public Health Agency Member States (CMS). Using the Oxford Nanopore Technologies MinION sequencing platform and ARTIC network sequencing protocols and bioinformatics pipeline, a total of 3610 SARS-CoV-2 positive RNA samples, received from 17 CMS, were sequenced in-situ during the period December 5th 2020 to December 31st 2021. Ninety-one Pango lineages, including those of five variants of concern (VOC), were identified. Genetic analysis revealed at least 260 introductions to the CMS from other global regions. For each of the 17 CMS, the percentage of reported COVID-19 cases sequenced by the COVID-19 IMPACT laboratory ranged from 0·02% to 3·80% (median = 1·12%). Sequences submitted to GISAID by our study represented 73·3% of all SARS-CoV-2 sequences from the 17 CMS available on the database up to December 31st 2021. Increased staffing, process and infrastructural improvement over the course of the project helped reduce turnaround times for reporting to originating institutions and sequence uploads to GISAID. Insights from our genomic surveillance network in the Caribbean region directly influenced non-pharmaceutical countermeasures in the CMS countries. However, limited availability of associated surveillance and clinical data made it challenging to contextualise the observed SARS-CoV-2 diversity and evolution, highlighting the need for development of infrastructure for collecting and integrating genomic sequencing data and sample-associated metadata.

Dataset Information

Metagenomic Pathogen Sequencing in Resource-Scarce Settings: Lessons Learned and the Road Ahead.

Publications

Metagenomic Pathogen Sequencing in Resource-Scarce Settings: Lessons Learned and the Road Ahead.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets