A pan-African pathogen genomics data sharing platform to support disease outbreaks

Christoffels, Alan; Mboowa, Gerald; van Heusden, Peter; Makhubela, Sello; Githinji, George; Mwangi, Sarah; Onywera, Harris; Nnaemeka, Ndodo; Amoako, Daniel Gyamfi; Olawoye, Idowu; Diallo, Amadou; Mbala-Kingebeni, Placide; Oyola, Samuel O.; Adu, Bright; Mvelase, Christopher; Ondoa, Pascale; Dratibi, Fred Athanasius; Sow, Abdourahmane; Gumede, Nicksy; Tessema, Sofonias K.; Ouma, Ahmed Ogwell; Tebeje, Yenew Kebede

doi:10.1038/s41591-023-02266-y

Cited by 10 publications

(6 citation statements)

References 24 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…5 and 6 . This reliance results from the shortage of local expertise and inadequate facilities and capacities for independent NGS data analysis [ 7 ]. While collaboration with international partners has been instrumental in implementing pathogen NGS and narrowing gaps with global Northern countries, building and expanding local sequencing, computing, and NGS analysis capacity is essential for a sustainable pathogen genomics and bioinformatics landscape [ 35 ].…”

Section: Discussionmentioning

confidence: 99%

“…The latest advancements in NGS technologies have paved the way for unprecedented pathogen surveillance, molecular epidemiology, and targeted public health interventions. Pathogen whole-genome sequencing (WGS) has been established as a powerful tool for unraveling the genomic landscape of microbial pathogens, providing intricate insights into their genetic makeup, evolution, and diversity [ 7 – 10 ]. This opens new avenues for detecting and responding quickly and effectively to disease threats and outbreaks [ 11 – 13 ].…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Assessment of the pathogen genomics landscape highlights disparities and challenges for effective AMR Surveillance and outbreak response in the East African community

Nguinkal,

Zoclanclounon,

Molina

et al. 2024

BMC Public Health

View full text Add to dashboard Cite

The East African Community (EAC) grapples with many challenges in tackling infectious disease threats and antimicrobial resistance (AMR), underscoring the importance of regional and robust pathogen genomics capacities. However, a significant disparity exists among EAC Partner States in harnessing bacterial pathogen sequencing and data analysis capabilities for effective AMR surveillance and outbreak response. This study assesses the current landscape and challenges associated with pathogen next-generation sequencing (NGS) within EAC, explicitly focusing on World Health Organization (WHO) AMR-priority pathogens. The assessment adopts a comprehensive approach, integrating a questionnaire-based survey amongst National Public Health Laboratories (NPHLs) with an analysis of publicly available metadata on bacterial pathogens isolated in the EAC countries. In addition to the heavy reliance on third-party organizations for bacterial NGS, the findings reveal a significant disparity among EAC member States in leveraging bacterial pathogen sequencing and data analysis. Approximately 97% (n = 4,462) of publicly available high-quality bacterial genome assemblies of samples collected in the EAC were processed and analyzed by external organizations, mainly in Europe and North America. Tanzania led in-country sequencing efforts, followed by Kenya and Uganda. The other EAC countries had no publicly available samples or had all their samples sequenced and analyzed outside the region. Insufficient local NGS sequencing facilities, limited bioinformatics expertise, lack of adequate computing resources, and inadequate data-sharing mechanisms are among the most pressing challenges that hinder the EAC’s NPHLs from effectively leveraging pathogen genomics data. These insights emphasized the need to strengthen microbial pathogen sequencing and data analysis capabilities within the EAC to empower these laboratories to conduct pathogen sequencing and data analysis independently. Substantial investments in equipment, technology, and capacity-building initiatives are crucial for supporting regional preparedness against infectious disease outbreaks and mitigating the impact of AMR burden. In addition, collaborative efforts should be developed to narrow the gap, remedy regional imbalances, and harmonize NGS data standards. Supporting regional collaboration, strengthening in-country genomics capabilities, and investing in long-term training programs will ultimately improve pathogen data generation and foster a robust NGS-driven AMR surveillance and outbreak response in the EAC, thereby supporting global health initiatives.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Assessment of the pathogen genomics landscape highlights disparities and challenges for effective AMR Surveillance and outbreak response in the East African community

Nguinkal,

Zoclanclounon,

Molina

et al. 2024

BMC Public Health

View full text Add to dashboard Cite

show abstract

“…Many studies suggested new advanced methods and study designs to minimize the impact of confounders, such as self-controlled designs [ 18 , 58 ] which automatically address time-invariant confounders. We argue combined data sources using innovative data modeling approaches would be globally imperative [ 66 , 67 , 68 ]. We strongly advise researchers to adhere to the reporting standards, such as REporting of studies Conducted using Observational Routinely collected health Data (RECORD) [ 21 ], so that readers can easily grasp the methodology and research findings.…”

Section: Discussionmentioning

confidence: 99%

COVID-19 Vaccine Safety Monitoring Studies in Low- and Middle-Income Countries (LMICs)—A Systematic Review of Study Designs and Methods

et al. 2023

View full text Add to dashboard Cite

Background: Post-marketing vaccine safety surveillance aims to monitor and quantify adverse events following immunization in a population, but little is known about their implementation in low- and middle-income countries (LMICs). We aimed to synthesize methodological approaches used to assess adverse events following COVID-19 vaccination in LMICs. Methods: For this systematic review, we searched articles published from 1 December 2019 to 18 February 2022 in main databases, including MEDLINE and Embase. We included all peer-reviewed observational COVID-19 vaccine safety monitoring studies. We excluded randomized controlled trials and case reports. We extracted data using a standardized extraction form. Two authors assessed study quality using the modified Newcastle–Ottawa Quality Assessment Scale. All findings were summarized narratively using frequency tables and figures. Results: Our search found 4254 studies, of which 58 were eligible for analysis. Many of the studies included in this review were conducted in middle-income countries, with 26 studies (45%) in lower-middle-income and 28 (48%) in upper-middle-income countries. More specifically, 14 studies were conducted in the Middle East region, 16 in South Asia, 8 in Latin America, 8 in Europe and Central Asia, and 4 in Africa. Only 3% scored 7–8 points (good quality) on the Newcastle–Ottawa Scale methodological quality assessment, while 10% got 5–6 points (medium). About 15 studies (25.9%) used a cohort study design and the rest were cross-sectional. In half of them (50%), vaccination data were gathered from the participants’ self-reporting methods. Seventeen studies (29.3%) used multivariable binary logistic regression and three (5.2%) used survival analyses. Only 12 studies (20.7%) performed model diagnostics and validity checks (e.g., the goodness of fit, identification of outliers, and co-linearity). Conclusions: Published studies on COVID-19 vaccine safety surveillance in LMICs are limited in number and the methods used do not often address potential confounders. Active surveillance of vaccines in LMICs are needed to advocate vaccination programs. Implementing training programs in pharmacoepidemiology in LMICs is essential.

show abstract

“… 19 , 20 , 21 Fifthly, all players should embrace guiding principles and standards for pathogen genomic data sharing that are ethical, egalitarian, efficient, and effective to inform public health policy and response. 8 , 9 , 22 , 23 …”

Section: Way Forwardmentioning

confidence: 99%

“…8,9,22,23 Africa is on the right track, having established programmes supporting pathogen genomic initiatives. For example, the Africa Centres for Disease Control and Prevention through the Africa Pathogen Genomics Initiative and the African Academy of Sciences are programmes that promote scientific and technological development in Africa while supporting public health pathogen genomics and bioinformatics.…”

mentioning

confidence: 99%

Why pathogen genomics is crucial in Africa’s public health

Mwapagha

2023

African Journal of Laboratory Medicine

View full text Add to dashboard Cite

show abstract

A pan-African pathogen genomics data sharing platform to support disease outbreaks

Cited by 10 publications

References 24 publications

Assessment of the pathogen genomics landscape highlights disparities and challenges for effective AMR Surveillance and outbreak response in the East African community

Assessment of the pathogen genomics landscape highlights disparities and challenges for effective AMR Surveillance and outbreak response in the East African community

COVID-19 Vaccine Safety Monitoring Studies in Low- and Middle-Income Countries (LMICs)—A Systematic Review of Study Designs and Methods

Why pathogen genomics is crucial in Africa’s public health

Contact Info

Product

Resources

About