Mosquito Abundance, Bed net Coverage and Other Factors Associated with Variations in Sporozoite Infectivity Rates in Four Villages of Rural Tanzania.

Entomological surveys are of great importance in decision-making processes regarding malaria control strategies because they help to identify associations between vector abundance both species-specific ecology and disease intervention factors associated with malaria transmission. Sporozoite infectivity rates, mosquito host blood meal source, bed net coverage and mosquito abundance were assessed in this study. A longitudinal survey was conducted in four villages in two regions of Tanzania. Malaria vectors were sampled using the CDC light trap and pyrethrum spray catch methods. In each village, ten paired houses were selected for mosquitoes sampling. Sampling was done in fortnight case and study was undertaken for six months in both Kilimanjaro (Northern Tanzania) and Dodoma (Central Tanzania) regions. A total of 6,883 mosquitoes were collected including: 5,628 (81.8%) Anopheles arabiensis, 1,100 (15.9%) Culex quinquefasciatus, 89 (1.4%) Anopheles funestus, and 66 (0.9%) Anopheles gambiae s.s. Of the total mosquitoes collected 3,861 were captured by CDC light trap and 3,022 by the pyrethrum spray catch method. The overall light trap: spray catch ratio was 1.3:1. Mosquito densities per room were 96.5 and 75.5 for light trap and pyrethrum spray catch respectively. Mosquito infectivity rates between villages that have high proportion of bed net owners and those without bed nets was significant (P < 0.001) and there was a significant difference in sporozoite rates between households with and without bed nets in these four villages (P < 0.001). Malaria remains a major problem in the study areas characterized as low transmission sites. Further studies are required to establish the annual entomological inoculation rates and to observe the annual parasitaemia dynamics in these communities. Outdoor mosquitoes collection should also be considered

The dominant Anopheles vectors of human malaria in Africa, Europe and the Middle East: occurrence data, distribution maps and bionomic précis

<p>Abstract</p> <p>Background</p> <p>This is the second in a series of three articles documenting the geographical distribution of 41 dominant vector species (DVS) of human malaria. The first paper addressed the DVS of the Americas and the third will consider those of the Asian Pacific Region. Here, the DVS of Africa, Europe and the Middle East are discussed. The continent of Africa experiences the bulk of the global malaria burden due in part to the presence of the <it>An. gambiae </it>complex. <it>Anopheles gambiae </it>is one of four DVS within the <it>An. gambiae </it>complex, the others being <it>An. arabiensis </it>and the coastal <it>An. merus </it>and <it>An. melas</it>. There are a further three, highly anthropophilic DVS in Africa, <it>An. funestus</it>, <it>An. moucheti </it>and <it>An. nili</it>. Conversely, across Europe and the Middle East, malaria transmission is low and frequently absent, despite the presence of six DVS. To help control malaria in Africa and the Middle East, or to identify the risk of its re-emergence in Europe, the contemporary distribution and bionomics of the relevant DVS are needed.</p> <p>Results</p> <p>A contemporary database of occurrence data, compiled from the formal literature and other relevant resources, resulted in the collation of information for seven DVS from 44 countries in Africa containing 4234 geo-referenced, independent sites. In Europe and the Middle East, six DVS were identified from 2784 geo-referenced sites across 49 countries. These occurrence data were combined with expert opinion ranges and a suite of environmental and climatic variables of relevance to anopheline ecology to produce predictive distribution maps using the Boosted Regression Tree (BRT) method.</p> <p>Conclusions</p> <p>The predicted geographic extent for the following DVS (or species/suspected species complex*) is provided for Africa: <it>Anopheles </it>(<it>Cellia</it>) <it>arabiensis</it>, <it>An. </it>(<it>Cel.</it>) <it>funestus*</it>, <it>An. </it>(<it>Cel.</it>) <it>gambiae</it>, <it>An. </it>(<it>Cel.</it>) <it>melas</it>, <it>An. </it>(<it>Cel.</it>) <it>merus</it>, <it>An. </it>(<it>Cel.</it>) <it>moucheti </it>and <it>An. </it>(<it>Cel.</it>) <it>nili*</it>, and in the European and Middle Eastern Region: <it>An. </it>(<it>Anopheles</it>) <it>atroparvus</it>, <it>An. </it>(<it>Ano.</it>) <it>labranchiae</it>, <it>An. </it>(<it>Ano.</it>) <it>messeae</it>, <it>An. </it>(<it>Ano.</it>) <it>sacharovi</it>, <it>An. </it>(<it>Cel.</it>) <it>sergentii </it>and <it>An. </it>(<it>Cel.</it>) <it>superpictus*</it>. These maps are presented alongside a bionomics summary for each species relevant to its control.</p

Genomic exploration using the ICEFinder tool reveals the strong predominance and extreme diversity of streptococcal ICEs and IMEs

Les éléments génétiques mobiles contribuent grandement à la diversité et à l’évolution des génomes bactériens par le biais du transfert horizontal. Parmi eux, les éléments intégratifs conjugatifs (ICE) codent leur propre excision, leur transfert par conjugaison et leur intégration. En revanche, les éléments intégratifs et mobilisables (IME) ne sont autonomes que pour leur excision et intégration et ne codent seulement que certaines des protéines/fonctions (oriT) dont ils ont besoin pour leur transfert conjugatif. Par conséquent, les IME ont besoin d’un élément conjugatif « helper » pour se transférer. Malgré leur impact sur le flux des gènes et l’évolution des génomes, la prévalence des ICE reste peu étudiée et seulement très peu d’IME avaient été identifiés au début de cette étude. De plus, bien que plusieurs méthodes de détection des ilots génomiques existent, aucune d’elles n’est dédiée aux ICE ou aux IME. Ce qui ne facilite pas l’analyse exhaustive de ces éléments. Le genre Streptococcus appartient au phylum des firmicutes. La quasi-totalité des streptocoques sont des bactéries commensales ou pathogènes de l’homme et d’autres animaux. Aussi, 2 espèces de streptocoques sont utilisées en tant que ferments lactiques lors la production de laits fermentés et divers fromages. Globalement, le genre streptocoques représente un groupe d’intérêt pour l’homme, l’étude du flux de gènes au sein de ces organismes et l’impact qu’il peut avoir sur leur mode vie est primordiale. Au cours de cette thèse, nous avons recherché les ICE et les IME dans 124 souches de streptocoques appartenant à 27 espèces en utilisant une base de données de référence comportant des protéines dites « signatures » d’IME et d’ICE (de leurs modules de conjugaison/mobilisation et d’integration/excision). Cette analyse exhaustive a permis l’identification et la délimitation de 131 ICE ou ICE légèrement dégénérés et 144 IME. Tous ces éléments ont été délimités, ce qui nous a permis de déterminer leur spécificité d’intégration dans les génomes. Au total, 17 spécificités d’intégration ont été identifiées pour les ICE dont 8 encore jamais décrites (ftsK, guaA, lysS, mutT, rpmG, rpsI, traG and ybaB/EbfC) et 18 spécificités pour les IME dont seulement 5 étaient connues chez les firmicutes. Les modules d’intégration des ICE codent soit une intégrase à tyrosine pouvant avoir une faible spécificité (1 famille d’intégrase) ou une forte spécificité (13 spécificités différentes), soit des intégrases à sérine seule ou en triplet (4 spécificités différentes), soit une transposase à DDE. Les IME codent soit des intégrases à tyrosine (10 spécificités différentes) soit des intégrases à serine seule (8 spécificités différentes). Les ICE ont été groupés en 7 familles distinctes selon les protéines codées par leur module de conjugaison. Les IME présentaient une très forte diversité au sein de leur module de mobilisation, empêchant ainsi leur regroupement en famille selon les gènes portés par ce module. Les analyses phylogénétiques des protéines signature codées par tous les ICE et les IME ont montré des échanges de modules d’intégration entre les ICE et les IME et de nombreux échanges entre les modules de mobilisation des IME. L’ensemble de ces résultats révèle la forte prévalence et l’extrême diversité des ICE et des IME au sein des génomes de streptocoques. Une meilleure connaissance et compréhension de ces éléments nous a incité à construire un outil informatique semi-automatisé de détection des ICE et des IME de Streptocoques ainsi que leurs sites d’insertionMobile genetic elements largely contribute to the evolution and diversity of bacterial genomes through horizontal gene transfer. Among them, the integrative and conjugative elements (ICEs) encode their own excision, conjugative transfer and integration. On the other hand, integrative mobilizable elements (IMEs) are autonomous for excision and integration but encode only some of the proteins needed for their conjugative transfer. IMEs therefore need a “helper” conjugative element to transfer. Despite their impact on gene flow and genome dynamics, the prevalence of ICEs remains largely underscored and very few IMEs were identified at the beginning of this study. Furthermore, although several in silico methods exist to detect genomic islands, none are dedicated to ICEs or IMEs, thus complicating exhaustive examination of these mobile elements. The Streptococcus genus belongs to the firmicutes’ phylum. Almost all streptococci are commensal bacteria or pathogenes to men and animals. Two species of Streptococcus are also used in the dairy industry as lactic ferments in order to produce fermented milk and different types of cheese. Studying the gene flux of the Steptococci genus and the impact it can have on the lifestyle of these organisms is essential, as it has a lot of interest for human health and activities. In this work, we searched for ICEs and IMEs in 124 strains of streptococci belonging to 27 species using a reference database of ICE and IME signature proteins (from their conjugation, mobilization and integration/excision modules). This exhaustive analysis led to the identification and delimitation of 131 ICEs or slightly decayed ICEs and 144 IMEs. All these elements were delimited, which allowed us to identify their integration specificities in the genomes. In total, 17 ICE integration specificities were identified. Among them, 8 had never been described before (ftsK, guaA, lysS, mutT, rpmG, rpsI, traG and ybaB/EbfC). 18 specificities were also identified for IMEs, among which only 5 were known for the firmicutes. ICEs encode high or low-specificity tyrosine integrases (13 different specificities), single serine intégrases (1 specificity), triplet of serine integrases (3 different specificities), or DDE transposases while IMEs encode either tyrosine integrases (10 different specificities) or single serine integrases (8 different specificities). ICE were grouped in 7 distinct families according to the proteins encoded by their conjugation module whereas the mobilization modules of IMEs were highly diverse, preventing them from grouping into families according to their mobilization modules. The phylogenetic analysis of the signature proteins encoded by all ICEs and IMEs showed integration module exchanges between ICEs and IMEs and several mobilization module exchanges between IMEs. The overall results reveal a strong prevalence and extreme diversity of these elements among Streptococci genomes. Better understanding and knowledge of ICEs and IMEs prompted us to build a semi-automated command-line tool to identify streptococcal ICEs and IMEs as well as to determine their insertion sit

L'exploration des génomes par l'outil ICEFinder révèle la forte prévalence et l'extrême diversité des ICE et des IME de streptocoques

Mobile genetic elements largely contribute to the evolution and diversity of bacterial genomes through horizontal gene transfer. Among them, the integrative and conjugative elements (ICEs) encode their own excision, conjugative transfer and integration. On the other hand, integrative mobilizable elements (IMEs) are autonomous for excision and integration but encode only some of the proteins needed for their conjugative transfer. IMEs therefore need a “helper” conjugative element to transfer. Despite their impact on gene flow and genome dynamics, the prevalence of ICEs remains largely underscored and very few IMEs were identified at the beginning of this study. Furthermore, although several in silico methods exist to detect genomic islands, none are dedicated to ICEs or IMEs, thus complicating exhaustive examination of these mobile elements. The Streptococcus genus belongs to the firmicutes’ phylum. Almost all streptococci are commensal bacteria or pathogenes to men and animals. Two species of Streptococcus are also used in the dairy industry as lactic ferments in order to produce fermented milk and different types of cheese. Studying the gene flux of the Steptococci genus and the impact it can have on the lifestyle of these organisms is essential, as it has a lot of interest for human health and activities. In this work, we searched for ICEs and IMEs in 124 strains of streptococci belonging to 27 species using a reference database of ICE and IME signature proteins (from their conjugation, mobilization and integration/excision modules). This exhaustive analysis led to the identification and delimitation of 131 ICEs or slightly decayed ICEs and 144 IMEs. All these elements were delimited, which allowed us to identify their integration specificities in the genomes. In total, 17 ICE integration specificities were identified. Among them, 8 had never been described before (ftsK, guaA, lysS, mutT, rpmG, rpsI, traG and ybaB/EbfC). 18 specificities were also identified for IMEs, among which only 5 were known for the firmicutes. ICEs encode high or low-specificity tyrosine integrases (13 different specificities), single serine intégrases (1 specificity), triplet of serine integrases (3 different specificities), or DDE transposases while IMEs encode either tyrosine integrases (10 different specificities) or single serine integrases (8 different specificities). ICE were grouped in 7 distinct families according to the proteins encoded by their conjugation module whereas the mobilization modules of IMEs were highly diverse, preventing them from grouping into families according to their mobilization modules. The phylogenetic analysis of the signature proteins encoded by all ICEs and IMEs showed integration module exchanges between ICEs and IMEs and several mobilization module exchanges between IMEs. The overall results reveal a strong prevalence and extreme diversity of these elements among Streptococci genomes. Better understanding and knowledge of ICEs and IMEs prompted us to build a semi-automated command-line tool to identify streptococcal ICEs and IMEs as well as to determine their insertion siteLes éléments génétiques mobiles contribuent grandement à la diversité et à l’évolution des génomes bactériens par le biais du transfert horizontal. Parmi eux, les éléments intégratifs conjugatifs (ICE) codent leur propre excision, leur transfert par conjugaison et leur intégration. En revanche, les éléments intégratifs et mobilisables (IME) ne sont autonomes que pour leur excision et intégration et ne codent seulement que certaines des protéines/fonctions (oriT) dont ils ont besoin pour leur transfert conjugatif. Par conséquent, les IME ont besoin d’un élément conjugatif « helper » pour se transférer. Malgré leur impact sur le flux des gènes et l’évolution des génomes, la prévalence des ICE reste peu étudiée et seulement très peu d’IME avaient été identifiés au début de cette étude. De plus, bien que plusieurs méthodes de détection des ilots génomiques existent, aucune d’elles n’est dédiée aux ICE ou aux IME. Ce qui ne facilite pas l’analyse exhaustive de ces éléments. Le genre Streptococcus appartient au phylum des firmicutes. La quasi-totalité des streptocoques sont des bactéries commensales ou pathogènes de l’homme et d’autres animaux. Aussi, 2 espèces de streptocoques sont utilisées en tant que ferments lactiques lors la production de laits fermentés et divers fromages. Globalement, le genre streptocoques représente un groupe d’intérêt pour l’homme, l’étude du flux de gènes au sein de ces organismes et l’impact qu’il peut avoir sur leur mode vie est primordiale. Au cours de cette thèse, nous avons recherché les ICE et les IME dans 124 souches de streptocoques appartenant à 27 espèces en utilisant une base de données de référence comportant des protéines dites « signatures » d’IME et d’ICE (de leurs modules de conjugaison/mobilisation et d’integration/excision). Cette analyse exhaustive a permis l’identification et la délimitation de 131 ICE ou ICE légèrement dégénérés et 144 IME. Tous ces éléments ont été délimités, ce qui nous a permis de déterminer leur spécificité d’intégration dans les génomes. Au total, 17 spécificités d’intégration ont été identifiées pour les ICE dont 8 encore jamais décrites (ftsK, guaA, lysS, mutT, rpmG, rpsI, traG and ybaB/EbfC) et 18 spécificités pour les IME dont seulement 5 étaient connues chez les firmicutes. Les modules d’intégration des ICE codent soit une intégrase à tyrosine pouvant avoir une faible spécificité (1 famille d’intégrase) ou une forte spécificité (13 spécificités différentes), soit des intégrases à sérine seule ou en triplet (4 spécificités différentes), soit une transposase à DDE. Les IME codent soit des intégrases à tyrosine (10 spécificités différentes) soit des intégrases à serine seule (8 spécificités différentes). Les ICE ont été groupés en 7 familles distinctes selon les protéines codées par leur module de conjugaison. Les IME présentaient une très forte diversité au sein de leur module de mobilisation, empêchant ainsi leur regroupement en famille selon les gènes portés par ce module. Les analyses phylogénétiques des protéines signature codées par tous les ICE et les IME ont montré des échanges de modules d’intégration entre les ICE et les IME et de nombreux échanges entre les modules de mobilisation des IME. L’ensemble de ces résultats révèle la forte prévalence et l’extrême diversité des ICE et des IME au sein des génomes de streptocoques. Une meilleure connaissance et compréhension de ces éléments nous a incité à construire un outil informatique semi-automatisé de détection des ICE et des IME de Streptocoques ainsi que leurs sites d’insertio

NAR Breakthrough Article Origins of transfer establish networks of functional dependencies for plasmid transfer by conjugation

International audiencePlasmids can be transferred between cells by conjugation, thereby driving bacterial evolution by horizontal gene transfer. Yet, we ignore the molecular mechanisms of transfer for many plasmids because they lack all protein-coding genes required for conjugation. We solved this conundrum by identifying hundreds of plasmids and chromosomes with conjugative origins of transfer in Escherichia coli and Staphylococcus aureus. These plasmids (pOriT) hijack the relaxases of conjugative or mobilizable elements, but not both. The functional dependencies between pOriT and other plasmids explain their cooccurrence: pOriT are abundant in cells with many plasmids, whereas conjugative plasmids are the most common in the others. We systematically characterized plasmid mobility in relation to conjugation and alternative mechanisms of transfer and can now propose a putative mechanism of transfer for ∼90% of them. In most cases, plasmid mobility seems to involve conjugation. Interestingly, the mechanisms of mobility are important determinants of plasmidencoded accessory traits, since pOriTs have the highest densities of antimicrobial resistance genes, whereas plasmids lacking putative mechanisms of transfer have the lowest. We illuminate the evolutionary relationships between plasmids and suggest that many pOriT may have arisen by gene deletions in other types of plasmids. These results suggest that most plasmids can be transferred by conjugation

The Obscure World of Integrative and Mobilizable Elements, Highly Widespread Elements that Pirate Bacterial Conjugative Systems

Conjugation is a key mechanism of bacterial evolution that involves mobile genetic elements. Recent findings indicated that the main actors of conjugative transfer are not the well-known conjugative or mobilizable plasmids but are the integrated elements. This paper reviews current knowledge on “integrative and mobilizable elements” (IMEs) that have recently been shown to be highly diverse and highly widespread but are still rarely described. IMEs encode their own excision and integration and use the conjugation machinery of unrelated co-resident conjugative element for their own transfer. Recent studies revealed a much more complex and much more diverse lifecycle than initially thought. Besides their main transmission as integrated elements, IMEs probably use plasmid-like strategies to ensure their maintenance after excision. Their interaction with conjugative elements reveals not only harmless hitchhikers but also hunters that use conjugative elements as target for their integration or harmful parasites that subvert the conjugative apparatus of incoming elements to invade cells that harbor them. IMEs carry genes conferring various functions, such as resistance to antibiotics, that can enhance the fitness of their hosts and that contribute to their maintenance in bacterial populations. Taken as a whole, IMEs are probably major contributors to bacterial evolution