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BACKGROUND: Dental caries remains the most prevalent non-communicable disease globally affecting 60–90% of children. The World Health Organisation's (WHO) health-promoting school program offers a framework for dental intervention in low- and middle-income countries (LMICs). This study explored teacher contributions to children's oral health in relation to the WHO health-promoting school framework in rural Uganda. METHODS: Semi structured interviews were conducted with a purposive sample of 18 teachers. All interviews were transcribed verbatim and analysed thematically. RESULTS: Many teachers reported preparing children to practise proper oral hygiene care through skills training and demonstrations around proper teeth brushing. Teachers' roles included raising health awareness by providing information on oral health topics using different educational methods. Many teachers mentioned performing oral health examinations on children at the school, first aid, referral for dental treatments and engaging parents, students and health workers in oral health promotion. CONCLUSIONS: Teachers play an essential role in oral health promotion in countries like Uganda. Teachers are implementing key principles of the WHO's health-promoting school framework on the ground and need to be considered as a key public health resource. If improvements in oral health are to be attained in Sub-Saharan Africa and other LMICs, government interventions need to harness teachers' contributions in delivering oral health promotion.

International audience ; We designed a PyQt graphical user interface-Sequanix-aimed at democratizing the use of Snakemake pipelines in the NGS space and beyond. By default, Sequanix includes Sequana NGS pipelines (Snakemake format) (http://sequana.readthedocs.io), and is also capable of loading any external Snakemake pipeline. New users can easily, visually, edit configuration files of expert-validated pipelines and can interactively execute these production-ready workflows. Sequanix will be useful to both Snakemake developers in exposing their pipelines and to a wide audience of users.

International audience ; We designed a PyQt graphical user interface-Sequanix-aimed at democratizing the use of Snakemake pipelines in the NGS space and beyond. By default, Sequanix includes Sequana NGS pipelines (Snakemake format) (http://sequana.readthedocs.io), and is also capable of loading any external Snakemake pipeline. New users can easily, visually, edit configuration files of expert-validated pipelines and can interactively execute these production-ready workflows. Sequanix will be useful to both Snakemake developers in exposing their pipelines and to a wide audience of users.

International audience ; We designed a PyQt graphical user interface-Sequanix-aimed at democratizing the use of Snakemake pipelines in the NGS space and beyond. By default, Sequanix includes Sequana NGS pipelines (Snakemake format) (http://sequana.readthedocs.io), and is also capable of loading any external Snakemake pipeline. New users can easily, visually, edit configuration files of expert-validated pipelines and can interactively execute these production-ready workflows. Sequanix will be useful to both Snakemake developers in exposing their pipelines and to a wide audience of users.

International audience ; We designed a PyQt graphical user interface-Sequanix-aimed at democratizing the use of Snakemake pipelines in the NGS space and beyond. By default, Sequanix includes Sequana NGS pipelines (Snakemake format) (http://sequana.readthedocs.io), and is also capable of loading any external Snakemake pipeline. New users can easily, visually, edit configuration files of expert-validated pipelines and can interactively execute these production-ready workflows. Sequanix will be useful to both Snakemake developers in exposing their pipelines and to a wide audience of users.

[Background]: Antimicrobial resistance is a major global health challenge. Metagenomics allows analyzing the presence and dynamics of "resistomes" (the ensemble of genes encoding antimicrobial resistance in a given microbiome) in disparate microbial ecosystems. However, the low sensitivity and specificity of available metagenomic methods preclude the detection of minority populations (often present below their detection threshold) and/or the identification of allelic variants that differ in the resulting phenotype. Here, we describe a novel strategy that combines targeted metagenomics using last generation in-solution capture platforms, with novel bioinformatics tools to establish a standardized framework that allows both quantitative and qualitative analyses of resistomes. [Methods]: We developed ResCap, a targeted sequence capture platform based on SeqCapEZ (NimbleGene) technology, which includes probes for 8667 canonical resistance genes (7963 antibiotic resistance genes and 704 genes conferring resistance to metals or biocides), and 2517 relaxase genes (plasmid markers) and 78,600 genes homologous to the previous identified targets (47,806 for antibiotics and 30,794 for biocides or metals). Its performance was compared with metagenomic shotgun sequencing (MSS) for 17 fecal samples (9 humans, 8 swine). ResCap significantly improves MSS to detect "gene abundance" (from 2.0 to 83.2%) and "gene diversity" (26 versus 14.9 genes unequivocally detected per sample per million of reads; the number of reads unequivocally mapped increasing up to 300-fold by using ResCap), which were calculated using novel bioinformatic tools. ResCap also facilitated the analysis of novel genes potentially involved in the resistance to antibiotics, metals, biocides, or any combination thereof. [Conclusions]: ResCap, the first targeted sequence capture, specifically developed to analyze resistomes, greatly enhances the sensitivity and specificity of available metagenomic methods and offers the possibility to analyze genes related to the selection and transfer of antimicrobial resistance (biocides, heavy metals, plasmids). The model opens the possibility to study other complex microbial systems in which minority populations play a relevant role. ; This study was supported by the European Commission, Seven Framework Program (EVOTARFP7-HEALTH-282004 for VFL, FB, JLM, AA, DE, ER, RJLW, WvS, FdlC, and TMC), the Joint Programming Initiative in Antimicrobial Resistance (JPIAMR Third call, STARCS, JPIAMR2016-AC16/00039 to TMC, RJLW, WvS), the Joint Programming Initiative in Water (JPI Water StARE JPIW2013-089-C02-01 to JLM) and the Ministry of Economy and Competitiveness of Spain (BIO2014-54507-R to JLM, and PLASWIRES-612146/FP7-ICT-2013-10 and BFU2014-55534-C2-1-P for FdlC). The authors also acknowledge the European Development Regional Fund "A way to achieve Europe" (ERDF) for co-founding the Spanish R&D National Plan 2012-2019 (BIO2014-54507-R to JLM, PI15-0512 to TMC, PI15-00818 to FB, and BFU2014-55534-C2-1-P to FdlC), CIBER (CIBER in Epidemiology and Public Health, CIBERESP; CB06/02/0053 to FB), the Spanish Network for Research on Infectious Diseases (REIPI RD12/0015 to JLM) and the Regional Government of Madrid (InGeMICS- B2017/BMD-3691). Val F. Lanza was further funded by a Research Award Grant 2016 of the European Society for Clinical Microbiology and Infectious Diseases (ESCMID). Additional funding was from the Metagenopolis grant ANR-11-DPBS-0001 to DE. ; Peer reviewed

BACKGROUND: Antimicrobial resistance is a major global health challenge. Metagenomics allows analyzing the presence and dynamics of "resistomes" (the ensemble of genes encoding antimicrobial resistance in a given microbiome) in disparate microbial ecosystems. However, the low sensitivity and specificity of available metagenomic methods preclude the detection of minority populations (often present below their detection threshold) and/or the identification of allelic variants that differ in the resulting phenotype. Here, we describe a novel strategy that combines targeted metagenomics using last generation in-solution capture platforms, with novel bioinformatics tools to establish a standardized framework that allows both quantitative and qualitative analyses of resistomes. METHODS: We developed ResCap, a targeted sequence capture platform based on SeqCapEZ (NimbleGene) technology, which includes probes for 8667 canonical resistance genes (7963 antibiotic resistance genes and 704 genes conferring resistance to metals or biocides), and 2517 relaxase genes (plasmid markers) and 78,600 genes homologous to the previous identified targets (47,806 for antibiotics and 30,794 for biocides or metals). Its performance was compared with metagenomic shotgun sequencing (MSS) for 17 fecal samples (9 humans, 8 swine). ResCap significantly improves MSS to detect "gene abundance" (from 2.0 to 83.2%) and "gene diversity" (26 versus 14.9 genes unequivocally detected per sample per million of reads; the number of reads unequivocally mapped increasing up to 300-fold by using ResCap), which were calculated using novel bioinformatic tools. ResCap also facilitated the analysis of novel genes potentially involved in the resistance to antibiotics, metals, biocides, or any combination thereof. CONCLUSIONS: ResCap, the first targeted sequence capture, specifically developed to analyze resistomes, greatly enhances the sensitivity and specificity of available metagenomic methods and offers the possibility to analyze genes related to the selection and transfer of antimicrobial resistance (biocides, heavy metals, plasmids). The model opens the possibility to study other complex microbial systems in which minority populations play a relevant role. ; This study was supported by the European Commission, Seven Framework Program (EVOTARFP7-HEALTH-282004 for VFL, FB, JLM, AA, DE, ER, RJLW, WvS, FdlC, and TMC), the Joint Programming Initiative in Antimicrobial Resistance (JPIAMR Third call, STARCS, JPIAMR2016-AC16/00039 to TMC, RJLW, WvS), the Joint Programming Initiative in Water (JPI Water StARE JPIW2013-089-C02-01 to JLM) and the Ministry of Economy and Competitiveness of Spain (BIO2014-54507-R to JLM, and PLASWIRES-612146/FP7-ICT-2013-10 and BFU2014-55534-C2-1-P for FdlC). The authors also acknowledge the European Development Regional Fund "A way to achieve Europe" (ERDF) for co-founding the Spanish R&D National Plan 2012-2019 (BIO2014-54507-R to JLM, PI15-0512 to TMC, PI15-00818 to FB, and BFU2014-55534-C2-1-P to FdlC), CIBER (CIBER in Epidemiology and Public Health, CIBERESP; CB06/02/0053 to FB), the Spanish Network for Research on Infectious Diseases (REIPI RD12/0015 to JLM) and the Regional Government of Madrid (InGeMICSB2017/BMD-3691). Val F. Lanza was further funded by a Research Award Grant 2016 of the European Society for Clinical Microbiology and Infectious Diseases (ESCMID). Additional funding was from the Metagenopolis grant ANR-11-DPBS-0001 to DE.