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Dans un contexte de profond renouvellement du système de recherche et d'enseignement supérieur, les opérateurs pertinent du domaine des sciences humaines et sociales, ensemble disciplinaire que l'on dit souvent insuffisamment organisé tant la tradition du travail individuel y est ancrée, ont en particulier à réfléchir sur les questions de structuration des SHS. On peut observer cette structuration et ses effets à divers niveaux : les personnes, les projets, les équipes, les institutions, et les réseaux. Pour ce faire, l'Alliance Athéna a mis en place un groupe « structuration des sciences de l'homme et de la société (SHS) », qui devait plus particulièrement travailler sur les questions suivantes : a) Mécanismes institutionnels de la concertation entre les acteurs pertinents pour la structuration de la recherche en SHS, b) Interfaces de la recherche SHS (SDV Sciences de la vie, Maths/STIC technologie de l'information et de la communication, Sciences de la terre.), c) Emploi scientifique SHS (gestion de l'emploi et des carrières par les opérateurs concernés) ; d) Politique des réseaux de recherche (en France, à l'échelle européenne, à l'échelle internationale), e) Rôle des MSH sur les sites (rapports avec la gouvernance de chaque site), à l'échelle nationale et internationale. Au fil de l'examen des différents thèmes, le groupe Structuration de l'alliance Athéna s'est emparé de la question d'équilibre entre une polarisation inéluctable du système de recherche et d'enseignement supérieur et le principe de développement partagé dont les universités implantées sur l'ensemble du territoire sont porteuses. Rapport dirigé par François Weil et Chantal Cases.

International audience ; Infection with Salmonella enterica serotype Typhimurium sequence type (ST) 313 is associated with high rates of drug resistance, bloodstream infections, and death. To determine whether ST313 is dominant in the Democratic Republic of the Congo, we studied 180 isolates collected during 2007-2011; 96% belonged to CRISPOL type CT28, which is associated with ST313.

Infection with Salmonella enterica serotype Typhimurium sequence type (ST) 313 is associated with high rates of drug resistance, bloodstream infections, and death. To determine whether ST313 is dominant in the Democratic Republic of the Congo, we studied 180 isolates collected during 2007–2011; 96% belonged to CRISPOL type CT28, which is associated with ST313.

International audience ; Infection with Salmonella enterica serotype Typhimurium sequence type (ST) 313 is associated with high rates of drug resistance, bloodstream infections, and death. To determine whether ST313 is dominant in the Democratic Republic of the Congo, we studied 180 isolates collected during 2007-2011; 96% belonged to CRISPOL type CT28, which is associated with ST313.

International audience ; BACKGROUND:Salmonella enterica is a major global food-borne pathogen, causing life-threatening infections. Ciprofloxacin and extended-spectrum cephalosporins (ESCs) are the drugs of choice for severe infections. We previously reported a ciprofloxacin-resistant S. enterica serotype Kentucky (S Kentucky) ST198-X1 strain that emerged in Egypt and spread throughout Africa and the Middle East from 2002 to 2008. We aimed to monitor recent trends in the location of transmission and antimicrobial resistance of this strain.METHODS:We analysed isolates of S Kentucky collected by the French national surveillance system for salmonellosis in France from Jan 1, 2000, to Dec 31, 2011, and at two sites in Casablanca, Morocco, between Jan 1, 2003, and Dec 31, 2011. We analysed patterns of travel of patients infected with a ciprofloxacin-resistant strain of S Kentucky. We identified isolates showing resistance to ESCs or decreased susceptibility to carbapenems, characterised isolates by XbaI-pulsed field gel electrophoresis and multilocus sequence typing, and assessed mechanisms of bacterial resistance to antimicrobial drugs.FINDINGS:954 (1%) of 128,836 serotyped Salmonella spp isolates in France were identified as S Kentucky, as were 30 (13%) of 226 Salmonella spp isolates from Morocco. During 2000-08, 200 (40%) of 497 subculturable isolates of S Kentucky obtained in France were resistant to ciprofloxacin, compared with 376 (83%) of 455 isolates in 2009-11, suggesting a recent increase in ciprofloxacin resistance in France. Travel histories suggested S Kentucky infections originated predominantly in east Africa, north Africa, west Africa, and the Middle East, but also arose in India. We report several occurrences of acquisition of extended-spectrum β-lactamase (CTX-M-1, CTX-M-15), plasmid-encoded cephalosporinase (CMY-2), or carbapenemase (OXA-48, VIM-2) genes by ciprofloxacin-resistant isolates of S Kentucky ST198-X1 from the Mediterranean area since 2009. Many of these highly drug-resistant isolates were also resistant to most aminoglycosides, to co-trimoxazole (trimethoprim-sulfamethoxazole), and to azithromycin.INTERPRETATION:The potential risk to public health posed by ciprofloxacin-resistant S Kentucky ST198-X1 warrants its inclusion in national programmes for the control of S. enterica in food-producing animals, in particular in poultry.FUNDING:Institut Pasteur, Institut de Veille Sanitaire, Fondation pour la Recherche Médicale, French Government Investissement d'Avenir programme.

International audience ; BACKGROUND:Salmonella enterica is a major global food-borne pathogen, causing life-threatening infections. Ciprofloxacin and extended-spectrum cephalosporins (ESCs) are the drugs of choice for severe infections. We previously reported a ciprofloxacin-resistant S. enterica serotype Kentucky (S Kentucky) ST198-X1 strain that emerged in Egypt and spread throughout Africa and the Middle East from 2002 to 2008. We aimed to monitor recent trends in the location of transmission and antimicrobial resistance of this strain.METHODS:We analysed isolates of S Kentucky collected by the French national surveillance system for salmonellosis in France from Jan 1, 2000, to Dec 31, 2011, and at two sites in Casablanca, Morocco, between Jan 1, 2003, and Dec 31, 2011. We analysed patterns of travel of patients infected with a ciprofloxacin-resistant strain of S Kentucky. We identified isolates showing resistance to ESCs or decreased susceptibility to carbapenems, characterised isolates by XbaI-pulsed field gel electrophoresis and multilocus sequence typing, and assessed mechanisms of bacterial resistance to antimicrobial drugs.FINDINGS:954 (1%) of 128,836 serotyped Salmonella spp isolates in France were identified as S Kentucky, as were 30 (13%) of 226 Salmonella spp isolates from Morocco. During 2000-08, 200 (40%) of 497 subculturable isolates of S Kentucky obtained in France were resistant to ciprofloxacin, compared with 376 (83%) of 455 isolates in 2009-11, suggesting a recent increase in ciprofloxacin resistance in France. Travel histories suggested S Kentucky infections originated predominantly in east Africa, north Africa, west Africa, and the Middle East, but also arose in India. We report several occurrences of acquisition of extended-spectrum β-lactamase (CTX-M-1, CTX-M-15), plasmid-encoded cephalosporinase (CMY-2), or carbapenemase (OXA-48, VIM-2) genes by ciprofloxacin-resistant isolates of S Kentucky ST198-X1 from the Mediterranean area since 2009. Many of these highly drug-resistant isolates were also resistant to most aminoglycosides, to co-trimoxazole (trimethoprim-sulfamethoxazole), and to azithromycin.INTERPRETATION:The potential risk to public health posed by ciprofloxacin-resistant S Kentucky ST198-X1 warrants its inclusion in national programmes for the control of S. enterica in food-producing animals, in particular in poultry.FUNDING:Institut Pasteur, Institut de Veille Sanitaire, Fondation pour la Recherche Médicale, French Government Investissement d'Avenir programme.

International audience ; Despite a significant global burden of disease, there is still no vaccine against shigellosis widely available. One aim of the European Union funded STOPENTERICS consortium is to develop vaccine candidates against Shigella. Given the importance of translational vaccine coverage, here we aimed to characterise the Shigella strains being used by the consortium by whole genome sequencing, and report on the stability of strains cultured in different laboratories or through serial passage. We sequenced, de novo assembled and annotated 20 Shigella strains being used by the consortium. These comprised 16 different isolates belonging to 7 serotypes, and 4 derivative strains. Derivative strains from common isolates were manipulated in different laboratories or had undergone multiple passages in the same laboratory. Strains were mapped against reference genomes to detect SNP variation and phylogenetic analysis was performed. The genomes assembled into similar total lengths (range 4.14-4.83 Mbp) and had similar numbers of predicted coding sequences (average of 4,400). Mapping analysis showed the genetic stability of strains through serial passages and culturing in different laboratories, as well as varying levels of similarity to published reference genomes. Phylogenetic analysis revealed the presence of three main clades among the strains and published references, one containing the Shigella flexneri serotype 6 strains, a second containing the remaining S. flexneri serotypes and a third comprised of Shigella sonnei strains. This work increases the number of the publically available Shigella genomes available and specifically provides information on strains being used for vaccine development by STOPENTERICS. It also provides information on the variability among strains maintained in different laboratories and through serial passage. This work will guide the selection of strains for further vaccine development.

International audience ; Despite a significant global burden of disease, there is still no vaccine against shigellosis widely available. One aim of the European Union funded STOPENTERICS consortium is to develop vaccine candidates against Shigella. Given the importance of translational vaccine coverage, here we aimed to characterise the Shigella strains being used by the consortium by whole genome sequencing, and report on the stability of strains cultured in different laboratories or through serial passage. We sequenced, de novo assembled and annotated 20 Shigella strains being used by the consortium. These comprised 16 different isolates belonging to 7 serotypes, and 4 derivative strains. Derivative strains from common isolates were manipulated in different laboratories or had undergone multiple passages in the same laboratory. Strains were mapped against reference genomes to detect SNP variation and phylogenetic analysis was performed. The genomes assembled into similar total lengths (range 4.14-4.83 Mbp) and had similar numbers of predicted coding sequences (average of 4,400). Mapping analysis showed the genetic stability of strains through serial passages and culturing in different laboratories, as well as varying levels of similarity to published reference genomes. Phylogenetic analysis revealed the presence of three main clades among the strains and published references, one containing the Shigella flexneri serotype 6 strains, a second containing the remaining S. flexneri serotypes and a third comprised of Shigella sonnei strains. This work increases the number of the publically available Shigella genomes available and specifically provides information on strains being used for vaccine development by STOPENTERICS. It also provides information on the variability among strains maintained in different laboratories and through serial passage. This work will guide the selection of strains for further vaccine development.

International audience ; Despite a significant global burden of disease, there is still no vaccine against shigellosis widely available. One aim of the European Union funded STOPENTERICS consortium is to develop vaccine candidates against Shigella. Given the importance of translational vaccine coverage, here we aimed to characterise the Shigella strains being used by the consortium by whole genome sequencing, and report on the stability of strains cultured in different laboratories or through serial passage. We sequenced, de novo assembled and annotated 20 Shigella strains being used by the consortium. These comprised 16 different isolates belonging to 7 serotypes, and 4 derivative strains. Derivative strains from common isolates were manipulated in different laboratories or had undergone multiple passages in the same laboratory. Strains were mapped against reference genomes to detect SNP variation and phylogenetic analysis was performed. The genomes assembled into similar total lengths (range 4.14-4.83 Mbp) and had similar numbers of predicted coding sequences (average of 4,400). Mapping analysis showed the genetic stability of strains through serial passages and culturing in different laboratories, as well as varying levels of similarity to published reference genomes. Phylogenetic analysis revealed the presence of three main clades among the strains and published references, one containing the Shigella flexneri serotype 6 strains, a second containing the remaining S. flexneri serotypes and a third comprised of Shigella sonnei strains. This work increases the number of the publically available Shigella genomes available and specifically provides information on strains being used for vaccine development by STOPENTERICS. It also provides information on the variability among strains maintained in different laboratories and through serial passage. This work will guide the selection of strains for further vaccine development.

International audience ; To the Editor: Many thanks for your interesting and informative special section on infectious diseases in the Amazon Region (1). Your readers should also be interested in a little known, but extremely successful, sustainable health program that had its start in the Amazon. In 1942, the governments of Brazil and the United States agreed to establish a special service for public health (called the Serviço Especial de Saúde Pública). The purpose of this program was to improve health conditions in key areas in the Amazon, expedite the collection and export of native rubber, and counteract the growing influence of Nazi Germany in Latin America (2). The program spread to the Vale do Rio Doce, where there were resources of iron ore, mica, and optical quartz, which were important for the war effort. Although the program eventually moved to all states of Brazil, the Amazon program remained an important activity for ≈50 years before it was integrated into the Brazilian Ministry of Health (3). The program in the Amazon fo-cused primarily on infectious disease. It comprised programs of immunization , provision of small sustainable water systems, development of privy programs (sewer systems in the larger centers of population), malaria control , improvement of residences and living conditions for Chagas disease control, epidemiologic intelligence, and extensive training for auxiliary and professional personnel. The effects of this program are shown by the increase in life expectancy for all age groups, with an increase of >10 years for those childhood age groups for whom infectious disease control would have the greatest effect from 1939–1941 to 1950–1951 (4). This program contains many lessons for the planners of health and disease control projects in tropical, low-income countries.

International audience ; To the Editor: Many thanks for your interesting and informative special section on infectious diseases in the Amazon Region (1). Your readers should also be interested in a little known, but extremely successful, sustainable health program that had its start in the Amazon. In 1942, the governments of Brazil and the United States agreed to establish a special service for public health (called the Serviço Especial de Saúde Pública). The purpose of this program was to improve health conditions in key areas in the Amazon, expedite the collection and export of native rubber, and counteract the growing influence of Nazi Germany in Latin America (2). The program spread to the Vale do Rio Doce, where there were resources of iron ore, mica, and optical quartz, which were important for the war effort. Although the program eventually moved to all states of Brazil, the Amazon program remained an important activity for ≈50 years before it was integrated into the Brazilian Ministry of Health (3). The program in the Amazon fo-cused primarily on infectious disease. It comprised programs of immunization , provision of small sustainable water systems, development of privy programs (sewer systems in the larger centers of population), malaria control , improvement of residences and living conditions for Chagas disease control, epidemiologic intelligence, and extensive training for auxiliary and professional personnel. The effects of this program are shown by the increase in life expectancy for all age groups, with an increase of >10 years for those childhood age groups for whom infectious disease control would have the greatest effect from 1939–1941 to 1950–1951 (4). This program contains many lessons for the planners of health and disease control projects in tropical, low-income countries.

International audience ; To the Editor: Many thanks for your interesting and informative special section on infectious diseases in the Amazon Region (1). Your readers should also be interested in a little known, but extremely successful, sustainable health program that had its start in the Amazon. In 1942, the governments of Brazil and the United States agreed to establish a special service for public health (called the Serviço Especial de Saúde Pública). The purpose of this program was to improve health conditions in key areas in the Amazon, expedite the collection and export of native rubber, and counteract the growing influence of Nazi Germany in Latin America (2). The program spread to the Vale do Rio Doce, where there were resources of iron ore, mica, and optical quartz, which were important for the war effort. Although the program eventually moved to all states of Brazil, the Amazon program remained an important activity for ≈50 years before it was integrated into the Brazilian Ministry of Health (3). The program in the Amazon fo-cused primarily on infectious disease. It comprised programs of immunization , provision of small sustainable water systems, development of privy programs (sewer systems in the larger centers of population), malaria control , improvement of residences and living conditions for Chagas disease control, epidemiologic intelligence, and extensive training for auxiliary and professional personnel. The effects of this program are shown by the increase in life expectancy for all age groups, with an increase of >10 years for those childhood age groups for whom infectious disease control would have the greatest effect from 1939–1941 to 1950–1951 (4). This program contains many lessons for the planners of health and disease control projects in tropical, low-income countries.

International audience ; Salmonella enterica serotype Kentucky can be a common causative agent of salmonellosis, usually associated with consumption of contaminated poultry. Antimicrobial resistance (AMR) to multiple drugs, including ciprofloxacin, is an emerging problem within this serotype. We used whole-genome sequencing (WGS) to investigate the phylogenetic structure and AMR content of 121 S. enterica serotype Kentucky sequence type 198 isolates from five continents. Population structure was inferred using phylogenomic analysis and whole genomes were compared to investigate changes in gene content, with a focus on acquired AMR genes. Our analysis showed that multidrug-resistant (MDR) S. enterica serotype Kentucky isolates belonged to a single lineage, which we estimate emerged circa 1989 following the acquisition of the AMR-associated Salmonella genomic island (SGI) 1 (variant SGI1-K) conferring resistance to ampicillin, streptomycin, gentamicin, sulfamethoxazole and tetracycline. Phylo-geographical analysis indicates this clone emerged in Egypt before disseminating into Northern, Southern and Western Africa, then to the Middle East, Asia and the European Union. The MDR clone has since accumulated various substitution mutations in the quinolone-resistance-determining regions (QRDRs) of DNA gyrase (gyrA) and DNA topoisomerase IV (parC), such that most strains carry three QRDR mutations which together confer resistance to ciprofloxacin. The majority of AMR genes in the S. enterica serotype Kentucky genomes were carried either on plasmids or SGI structures. Remarkably, each genome of the MDR clone carried a different SGI1-K derivative structure; this variation could be attributed to IS26-mediated insertions and deletions , which appear to have hampered previous attempts to trace the clone's evolution using sub-WGS resolution approaches. Several different AMR plasmids were also identified, encoding resistance to chloramphenicol, third-generation cephalosporins, carbapenems and/or azithromycin. These results ...

International audience ; Salmonella enterica serotype Kentucky can be a common causative agent of salmonellosis, usually associated with consumption of contaminated poultry. Antimicrobial resistance (AMR) to multiple drugs, including ciprofloxacin, is an emerging problem within this serotype. We used whole-genome sequencing (WGS) to investigate the phylogenetic structure and AMR content of 121 S. enterica serotype Kentucky sequence type 198 isolates from five continents. Population structure was inferred using phylogenomic analysis and whole genomes were compared to investigate changes in gene content, with a focus on acquired AMR genes. Our analysis showed that multidrug-resistant (MDR) S. enterica serotype Kentucky isolates belonged to a single lineage, which we estimate emerged circa 1989 following the acquisition of the AMR-associated Salmonella genomic island (SGI) 1 (variant SGI1-K) conferring resistance to ampicillin, streptomycin, gentamicin, sulfamethoxazole and tetracycline. Phylo-geographical analysis indicates this clone emerged in Egypt before disseminating into Northern, Southern and Western Africa, then to the Middle East, Asia and the European Union. The MDR clone has since accumulated various substitution mutations in the quinolone-resistance-determining regions (QRDRs) of DNA gyrase (gyrA) and DNA topoisomerase IV (parC), such that most strains carry three QRDR mutations which together confer resistance to ciprofloxacin. The majority of AMR genes in the S. enterica serotype Kentucky genomes were carried either on plasmids or SGI structures. Remarkably, each genome of the MDR clone carried a different SGI1-K derivative structure; this variation could be attributed to IS26-mediated insertions and deletions , which appear to have hampered previous attempts to trace the clone's evolution using sub-WGS resolution approaches. Several different AMR plasmids were also identified, encoding resistance to chloramphenicol, third-generation cephalosporins, carbapenems and/or azithromycin. These results indicate that most MDR S. enterica serotype Kentucky circulating globally result from the clonal expansion of a single lineage that acquired chromosomal AMR genes 30 years ago, and has continued to diversify and accumulate additional resistances to last-line oral antimicrobials.

International audience ; Salmonella enterica serotype Kentucky can be a common causative agent of salmonellosis, usually associated with consumption of contaminated poultry. Antimicrobial resistance (AMR) to multiple drugs, including ciprofloxacin, is an emerging problem within this serotype. We used whole-genome sequencing (WGS) to investigate the phylogenetic structure and AMR content of 121 S. enterica serotype Kentucky sequence type 198 isolates from five continents. Population structure was inferred using phylogenomic analysis and whole genomes were compared to investigate changes in gene content, with a focus on acquired AMR genes. Our analysis showed that multidrug-resistant (MDR) S. enterica serotype Kentucky isolates belonged to a single lineage, which we estimate emerged circa 1989 following the acquisition of the AMR-associated Salmonella genomic island (SGI) 1 (variant SGI1-K) conferring resistance to ampicillin, streptomycin, gentamicin, sulfamethoxazole and tetracycline. Phylo-geographical analysis indicates this clone emerged in Egypt before disseminating into Northern, Southern and Western Africa, then to the Middle East, Asia and the European Union. The MDR clone has since accumulated various substitution mutations in the quinolone-resistance-determining regions (QRDRs) of DNA gyrase (gyrA) and DNA topoisomerase IV (parC), such that most strains carry three QRDR mutations which together confer resistance to ciprofloxacin. The majority of AMR genes in the S. enterica serotype Kentucky genomes were carried either on plasmids or SGI structures. Remarkably, each genome of the MDR clone carried a different SGI1-K derivative structure; this variation could be attributed to IS26-mediated insertions and deletions , which appear to have hampered previous attempts to trace the clone's evolution using sub-WGS resolution approaches. Several different AMR plasmids were also identified, encoding resistance to chloramphenicol, third-generation cephalosporins, carbapenems and/or azithromycin. These results ...