An accessible, efficient and global approach for the large-scale sequencing of bacterial genomes

AbstractWe have developed an efficient and inexpensive pipeline for streamlining large-scale collection and genome sequencing of bacterial isolates. Evaluation of this method involved a worldwide research collaboration focused on the model organism Salmonella enterica, the 10KSG consortium. By optimising a logistics pipeline that collected isolates as thermolysates, permitting shipment in ambient conditions, the project assembled a diverse collection of 10,419 clinical and environmental isolates from low- and middle-income countries in less than one year. The bacteria were obtained from 51 countries/territories dating from 1949 to 2017, with a focus on Africa and Latin-America. All isolates were collected in barcoded tubes and genome sequenced using an optimised DNA extraction method and the LITE pipeline for library construction. After Illumina sequencing, the total reagent cost was less than USD$10 per genome. Our method can be applied to genome-sequence other large bacterial collections at a relatively low cost, within a limited timeframe, to support global collaborations.

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Farming with Alternative Pollinators benefits pollinators, natural enemies, and yields, and offers transformative change to agriculture

Scientific Reports ◽

10.1038/s41598-021-97695-5 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Stefanie Christmann ◽

Youssef Bencharki ◽

Soukaina Anougmar ◽

Pierre Rasmont ◽

Moulay Chrif Smaili ◽

...

Keyword(s):

Large Scale ◽

Transformative Change ◽

Net Income ◽

Land Sharing ◽

Pollinator Decline ◽

Middle Income ◽

Land Sparing ◽

Middle Income Countries ◽

Small Grant ◽

Wildflower Strips

AbstractLow- and middle-income countries cannot afford reward-based land sparing for wildflower strips to combat pollinator decline. Two small-grant projects assessed, if an opportunity-cost saving land-sharing approach, Farming with Alternative Pollinators, can provide a method-inherent incentive to motivate farmers to protect pollinators without external rewards. The first large-scale Farming-with-Alternative-Pollinators project used seven main field crops in 233 farmer fields of four agro-ecosystems (adequate rainfall, semi-arid, mountainous and oasis) in Morocco. Here we show results: higher diversity and abundance of wild pollinators and lower pest abundance in enhanced fields than in monocultural control fields; the average net-income increase per surface is 121%. The higher income is a performance-related incentive to enhance habitats. The income increase for farmers is significant and the increase in food production is substantial. Higher productivity per surface can reduce pressure on (semi)-natural landscapes which are increasingly used for agriculture. Land-use change additionally endangers biodiversity and pollinators, whereas this new pollinator-protection approach has potential for transformative change in agriculture.

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The large-scale blast score ratio (LS-BSR) pipeline: a method to rapidly compare genetic content between bacterial genomes

10.7287/peerj.preprints.220v1 ◽

2014 ◽

Author(s):

Jason W Sahl ◽

Greg Caporaso ◽

David A Rasko ◽

Paul S Keim

Keyword(s):

Large Scale ◽

Sequence Data ◽

Parallel Implementation ◽

Genetic Relationships ◽

Clinical Diagnostics ◽

Whole Genome Sequence ◽

Bacterial Isolates ◽

Bacterial Genomes ◽

E Coli ◽

Blast Score

Background. As whole genome sequence data from bacterial isolates becomes cheaper to generate, computational methods are needed to correlate sequence data with biological observations. Here we present the large-scale BLAST score ratio (LS-BSR) pipeline, which rapidly compares the genetic content of hundreds to thousands of bacterial genomes, and returns a matrix that describes the relatedness of all coding sequences (CDSs) in all genomes surveyed. This matrix can be easily parsed in order to identify genetic relationships between bacterial genomes. Although pipelines have been published that group peptides by sequence similarity, no other software performs the large-scale, flexible, full-genome comparative analyses carried out by LS-BSR. Results. To demonstrate the utility of the method, the LS-BSR pipeline was tested on 96 Escherichia coli and Shigella genomes; the pipeline ran in 163 minutes using 16 processors, which is a greater than 7-fold speedup compared to using a single processor. The BSR values for each CDS, which indicate a relative level of relatedness, were then mapped to each genome on an independent core genome single nucleotide polymorphism (SNP) based phylogeny. Comparisons were then used to identify clade specific CDS markers and validate the LS-BSR pipeline based on molecular markers that delineate between classical E. coli pathogenic variant (pathovar) designations. Scalability tests demonstrated that the LS-BSR pipeline can process 1,000 E. coli genomes in ~60h using 16 processors. Conclusions. LS-BSR is an open-source, parallel implementation of the BSR algorithm, enabling rapid comparison of the genetic content of large numbers of genomes. The results of the pipeline can be used to identify specific markers between user-defined phylogenetic groups, and to identify the loss and/or acquisition of genetic information between bacterial isolates. Taxa-specific genetic markers can then be translated into clinical diagnostics, or can be used to identify broadly conserved putative therapeutic candidates.

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Improved micronutrient status and health outcomes in low- and middle-income countries following large-scale fortification: evidence from a systematic review and meta-analysis

Yearbook of Paediatric Endocrinology ◽

10.1530/ey.16.13.17 ◽

2019 ◽

Author(s):

Keats EC ◽

Neufeld LM ◽

Garrett GS ◽

Mbuya MNN ◽

Bhutta Z

Keyword(s):

Systematic Review ◽

Health Outcomes ◽

Large Scale ◽

Meta Analysis ◽

Middle Income ◽

Middle Income Countries ◽

Micronutrient Status ◽

Low And Middle Income

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Large-Scale Food Fortification and Biofortification in Low- and Middle-Income Countries: A Review of Programs, Trends, Challenges, and Evidence Gaps

Food and Nutrition Bulletin ◽

10.1177/0379572118774229 ◽

2018 ◽

Vol 39 (2) ◽

pp. 315-331 ◽

Cited By ~ 29

Author(s):

Saskia J. M. Osendarp ◽

Homero Martinez ◽

Greg S. Garrett ◽

Lynnette M. Neufeld ◽

Luz Maria De-Regil ◽

...

Keyword(s):

Large Scale ◽

Food System ◽

Food Fortification ◽

Micronutrient Deficiencies ◽

Middle Income ◽

Middle Income Countries ◽

Essential Components ◽

Quality Of Delivery ◽

And Control ◽

Low And Middle Income

Background: Food fortification and biofortification are well-established strategies to address micronutrient deficiencies in vulnerable populations. However, the effectiveness of fortification programs is not only determined by the biological efficacy of the fortified foods but also by effective and sustainable implementation, which requires continual monitoring, quality assurance and control, and corrective measures to ensure high compliance. Objective: To provide an overview of efficacy, effectiveness, economics of food fortification and biofortification, and status of and challenges faced by large-scale food fortification programs in low- and middle-income countries (LMIC). Methods: A literature review of PubMed publications in English from 2000 to 2017, as well as gray literature, targeting nongovernmental organizations whose work focuses on this topic, complemented by national reports and a “snowball” process of citation searching. The article describes remaining technical challenges, barriers, and evidence gap and prioritizes recommendations and next steps to further accelerate progress and potential of impact. Results: The review identifies and highlights essential components of successful programs. It also points out issues that determine poor program performance, including lack of adequate monitoring and enforcement and poor compliance with standards by industry. Conclusions: In the last 17 years, large-scale food fortification initiatives have been reaching increasingly larger segments of populations in LMIC. Large-scale food fortification and biofortification should be part of other nutrition-specific and nutrition-sensitive efforts to prevent and control micronutrient deficiencies. There are remaining technical and food system challenges, especially in relation to improving coverage and quality of delivery and measuring progress of national programs.

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Correlates of relationship issues among youth: Findings from a large scale youth mental health promotion program in India

10.21203/rs.3.rs-17841/v1 ◽

2020 ◽

Author(s):

Pradeep Banandur ◽

Gopalan Kalpana ◽

Shikha G Pai ◽

Mutharaju Arelingaiah ◽

Sathya R Velu ◽

...

Keyword(s):

Mental Health ◽

Health Promotion ◽

Large Scale ◽

Health Promotion Program ◽

Middle Income ◽

Factors Affecting ◽

Safety Issues ◽

Middle Income Countries ◽

Low Middle Income Countries ◽

Health Promotion Interventions

Abstract Background : Relationships and mental health have a bidirectional effect. The effect of relationships on mental health is stronger than vice versa. We analyzed two-year case records of 8595 beneficiaries aged 15-35 years attending youth guidance centres (Yuva Spandana Kendras) in Karnataka, India to understand factors affecting relationship issues. Methods : Multivariate logistic regression was performed with any beneficiary reporting having a relationship issue as outcome. Results : Occupation, marital status, health and lifestyle issues, personality issues, safety issues, gender, sex, & sexuality issues, suicidality, alcohol, and different emotions experienced,had significant association with relationship issues. Investing in health promotion interventions focusing on these precursors of relationship issues amongst youth seems strategic. Conclusion : Our findings have implications for other states in India and other low-middle-income countries like India.

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Perceived Trust and Confidence for Cryptocurrency Adoption

10.4018/978-1-7998-9035-5.ch014 ◽

2022 ◽

pp. 250-279

Author(s):

Ewilly Jie Ying Liew ◽

Wei Li Peh ◽

Zhuan Kee Leong

Keyword(s):

Large Scale ◽

Social Impact ◽

Public Perceptions ◽

Middle Income ◽

Individual Level ◽

Perceived Trust ◽

Middle Income Countries ◽

Regulatory Bodies ◽

The Individual ◽

National Databases

This chapter seeks to examine the influence of public perceptions of trust in people and confidence in institutions on cryptocurrency adoption, taking into account the individual-level demographic factors and the regional-level contextual factors. Data is obtained from three large-scale international surveys and national databases and analyzed using R software. The multivariate results demonstrate that individuals' public perceptions of trust and confidence significantly contribute to cryptocurrency adoption. Lower perceived trust in people and higher perceived confidence in civil service and international regulatory bodies increase cryptocurrency adoption, while perceived confidence in political and financial institutions discourages cryptocurrency adoption. Additionally, the univariate results find significant comparisons of gender and perceived trust differences on the predictors of cryptocurrency adoption. This chapter discusses and provides insights on the social impact and future of cryptocurrency adoption, particularly among the upper- and lower-middle-income countries.

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Election Administration, Resource Allocation, and Turnout: Evidence From Kenya

Comparative Political Studies ◽

10.1177/0010414020938083 ◽

2020 ◽

pp. 001041402093808

Author(s):

J. Andrew Harris

Keyword(s):

Decision Making ◽

Resource Allocation ◽

Political Behavior ◽

Large Scale ◽

Regression Discontinuity ◽

Regression Discontinuity Design ◽

Middle Income ◽

Election Administration ◽

Middle Income Countries ◽

Policy Choices

Decisions about how to organize and run an election can shape political participation. Policy choices may distribute election resources unequally, skewing voting outcomes. In low- and middle-income countries where electoral capacity and resources are scarce and decision-making highly centralized, election administration has the potential to shape results on a large scale. In the context of Kenya’s August 2017 elections, I study the consequences of a legislated threshold that determines the capacity of polling centers to quickly serve voters by reducing election-day lines. Using a regression discontinuity design, I find that turnout is 2.4% lower in congested polling places just below the threshold relative to polling places above the threshold. Relative to other hypothetical thresholds, the chosen threshold benefits the incumbent president, as incumbent strongholds receive more polling resources than opposition areas. The results demonstrate how electoral resource allocation shapes political behavior and election outcomes.

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Large-scale road safety programmes in low- and middle-income countries: An opportunity to generate evidence

Global Public Health ◽

10.1080/17441692.2013.769613 ◽

2013 ◽

Vol 8 (5) ◽

pp. 504-518 ◽

Cited By ~ 13

Author(s):

Adnan A. Hyder ◽

Katharine A. Allen ◽

David H. Peters ◽

Aruna Chandran ◽

David Bishai

Keyword(s):

Road Safety ◽

Large Scale ◽

Middle Income ◽

Middle Income Countries ◽

Low And Middle Income

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Stigma and discrimination related to mental illness in low- and middle-income countries

Epidemiology and Psychiatric Sciences ◽

10.1017/s2045796015000359 ◽

2015 ◽

Vol 24 (5) ◽

pp. 382-394 ◽

Cited By ~ 65

Author(s):

M. Semrau ◽

S. Evans-Lacko ◽

M. Koschorke ◽

L. Ashenafi ◽

G. Thornicroft

Keyword(s):

Mental Illness ◽

Large Scale ◽

Grey Literature ◽

Middle Income ◽

Middle Income Countries ◽

Stigma And Discrimination ◽

Effective Interventions ◽

Long Term Follow Up ◽

Context Specific ◽

Low And Middle Income

Aims.This paper aims to provide an overview of evidence from low- and middle-income countries (LAMICs) worldwide to address: the nature of stigma and discrimination, relevant context-specific factors, global patterns of these phenomena and their measurement and quantitative and qualitative evidence of interventions intended to reduce their occurrence and impact. The background to this study is that the large majority of studies concerned with identifying effective interventions to reduce stigma and discrimination originate in high-income countries (HICs). This paper therefore presents such evidence from, and relevant to, LAMICs.Methods.Conceptual overview of the relevant peer-reviewed and grey literature on stigma and discrimination related to mental illness in LAMICs are available in English, Spanish, French and Russian.Results.Few intervention studies were identified related to stigma re-education in LAMICs. None of these addressed behaviour change/discrimination, and there were no long-term follow-up studies. There is therefore insufficient evidence at present to know which overall types of intervention may be effective and feasible and in LAMICs, how best to target key groups such as healthcare staff, and how far they may need to be locally customised to be acceptable for large-scale use in these settings. In particular, forms of social contacts, which have been shown to be the most effective intervention to reduce stigma among adults in HICs, have not yet been assessed sufficiently to know whether these methods are also effective in LAMICs.Conclusion.Generating information about effective interventions to reduce stigma and discrimination in LAMICs is now an important mental health priority worldwide.

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