Phylogenetic reconstruction of transmission events from individuals with acute HIV infection: toward more-rigorous epidemiological definitions.

Phylogenetic reconstructions of transmission events from individuals with acute human immunodeficiency virus (HIV) infection are conducted to illustrate this group's heightened infectivity. Varied definitions of acute infection and assumptions about observed phylogenetic clusters may produce misleading results. We conducted a phylogenetic analysis of HIV pol sequences from 165 European patients with estimated infection dates and calculated the difference between dates within clusters. Nine phylogenetic clusters were observed. Comparison of dates within clusters revealed that only 2 could have been generated during acute infection. Previous analyses may have incorrectly assigned transmission events to the acutely HIV infected when they were more likely to have occurred during chronic infection.

Phylogenetic analysis of Biomphalaria tenagophila (Orbigny, 1835) (Mollusca: Gastropoda)

Mitochondrial DNA of Biomphalaria tenagophila, a mollusc intermediate host of Schistosoma mansoni in Brazil, was sequenced and characterised. The genome size found for B. tenagophila was 13,722 bp and contained 13 messenger RNAs, 22 transfer RNAs (tRNA) and two ribosomal RNAs (rRNA). In addition to sequencing, the mitochondrial DNA (mtDNA) genome organization of B. tenagophila was analysed based on its content and localization of both coding and non-coding regions, regions of gene overlap and tRNA nucleotide sequences. Sequences of protein, rRNA 12S and rRNA 16S nucleotides as well as gene organization were compared between B. tenagophila and Biomphalaria glabrata, as the latter is the most important S. mansoni intermediate host in Brazil. Differences between such species were observed regarding rRNA composition. The complete sequence of the B. tenagophila mitochondrial genome was deposited in GenBank (accession EF433576). Furthermore, phylogenetic relationships were estimated among 28 mollusc species, which had their complete mitochondrial genome deposited in GenBank, using the neighbour-joining method, maximum parsimony and maximum likelihood bootstrap. B. tenagophila was positioned at a branch close to B. glabrata and Pulmonata molluscs, collectively comprising a paraphyletic group, contrary to Opistobranchia, which was positioned at a single branch and constituted a monophyletic group.

DNA multigene sequencing of topotypic specimens of the fascioliasis vector Lymnaea diaphana and phylogenetic analysis of the genus Pectinidens (Gastropoda)

Freshwater lymnaeid snails are crucial in defining transmission and epidemiology of fascioliasis. In South America, human endemic areas are related to high altitudes in Andean regions. The species Lymnaea diaphana has, however, been involved in low altitude areas of Chile, Argentina and Peru where human infection also occurs. Complete nuclear ribosomal DNA 18S, internal transcribed spacer (ITS)-2 and ITS-1 and fragments of mitochondrial DNA 16S and cytochrome c oxidase (cox)1 genes of L. diaphana specimens from its type locality offered 1,848, 495, 520, 424 and 672 bp long sequences. Comparisons with New and Old World Galba/Fossaria, Palaearctic stagnicolines, Nearctic stagnicolines, Old World Radix and Pseudosuccinea allowed to conclude that (i) L. diaphana shows sequences very different from all other lymnaeids, (ii) each marker allows its differentiation, except cox1 amino acid sequence, and (iii) L. diaphana is not a fossarine lymnaeid, but rather an archaic relict form derived from the oldest North American stagnicoline ancestors. Phylogeny and large genetic distances support the genus Pectinidens as the first stagnicoline representative in the southern hemisphere, including colonization of extreme world regions, as most southern Patagonia, long time ago. The phylogenetic link of L. diaphana with the stagnicoline group may give light to the aforementioned peculiar low altitude epidemiological scenario of fascioliasis.

Evolution of Trypanosoma cruzi: clarifying hybridisations, mitochondrial introgressions and phylogenetic relationships between major lineages

Several different models of Trypanosoma cruzi evolution have been proposed. These models suggest that scarce events of genetic exchange occurred during the evolutionary history of this parasite. In addition, the debate has focused on the existence of one or two hybridisation events during the evolution of T. cruzi lineages. Here, we reviewed the literature and analysed available sequence data to clarify the phylogenetic relationships among these different lineages. We observed that TcI, TcIII and TcIV form a monophyletic group and that TcIII and TcIV are not, as previously suggested, TcI-TcII hybrids. Particularly, TcI and TcIII are sister groups that diverged around the same time that a widely distributed TcIV split into two clades (TcIVS and TcIVN). In addition, we collected evidence that TcIII received TcIVSkDNA by introgression on several occasions. Different demographic hypotheses (surfing and asymmetrical introgression) may explain the origin and expansion of the TcIII group. Considering these hypotheses, genetic exchange should have been relatively frequent between TcIII and TcIVS in the geographic area in which their distributions overlapped. In addition, our results support the hypothesis that two independent hybridisation events gave rise to TcV and TcVI. Consequently, TcIVS kDNA was first transferred to TcIII and later to TcV and TcVI in TcII/TcIII hybridisation events.

Molecular characterisation of the NSP4 gene of group A human rotavirus G2P[4] strains circulating in São Paulo, Brazil, from 1994 and 2006 to 2010

Group A human rotaviruses (HuRVA) are causative agents of acute gastroenteritis. Six viral structural proteins (VPs) and six nonstructural proteins (NSPs) are produced in RV-infected cells. NSP4 is a diarrhoea-inducing viral enterotoxin and NSP4 gene analysis revealed at least 15 (E1-E15) genotypes. This study analysed the NSP4 genetic diversity of HuRVA G2P[4] strains collected in the state of São Paulo (SP) from 1994 and 2006-2010 using reverse transcription-polymerase chain reaction, sequencing and phylogenetic analysis. Forty (97.6%) G2P[4] strains displayed genotype E2; one strain (2.4%) displayed genotype E1. These results are consistent with the proposed linkage between VP4/VP7 (G2P[4]) and the NSP4 (E2) genotype of HuRVA. NSP4 phylogenetic analysis showed distinct clusters, with grouping of most strains by their genotype and collection year, and most strains from SP were clustered together with strains from other Brazilian states. A deduced amino acid sequence alignment for E2 showed many variations in the C-terminal region, including the VP4-binding domain. Considering the ability of NSP4 to generate host immunity, monitoring NSP4 variations, along with those in the VP4 or VP7 protein, is important for evaluating the circulation and pathogenesis of RV. Finally, the presence of one G2P[4]E1 strain reinforces the idea that new genotype combinations emerge through reassortment and independent segregation.

Social meets molecular: Combining phylogenetic and latent class analyses to understand HIV-1 transmission in Switzerland.

Switzerland has a complex human immunodeficiency virus (HIV) epidemic involving several populations. We examined transmission of HIV type 1 (HIV-1) in a national cohort study. Latent class analysis was used to identify socioeconomic and behavioral groups among 6,027 patients enrolled in the Swiss HIV Cohort Study between 2000 and 2011. Phylogenetic analysis of sequence data, available for 4,013 patients, was used to identify transmission clusters. Concordance between sociobehavioral groups and transmission clusters was assessed in correlation and multiple correspondence analyses. A total of 2,696 patients were infected with subtype B, 203 with subtype C, 196 with subtype A, and 733 with recombinant subtypes (mainly CRF02_AG and CRF01_AE). Latent class analysis identified 8 patient groups. Most transmission clusters of subtype B were shared between groups of gay men (groups 1-3) or between the heterosexual groups "heterosexual people of lower socioeconomic position" (group 4) and "injection drug users" (group 8). Clusters linking homosexual and heterosexual groups were associated with "older heterosexual and gay people on welfare" (group 5). "Migrant women in heterosexual partnerships" (group 6) and "heterosexual migrants on welfare" (group 7) shared non-B clusters with groups 4 and 5. Combining approaches from social and molecular epidemiology can provide insights into HIV-1 transmission and inform the design of prevention strategies.

Shifts in species and phylogenetic diversity between sapling and tree communities indicate negative density dependence in a lowland rain forest

1. As trees in a given cohort progress through ontogeny, many individuals die. This risk of mortality is unevenly distributed across species because of many processes such as habitat filtering, interspecific competition and negative density dependence. Here, we predict and test the patterns that such ecological processes should inscribe on both species and phylogenetic diversity as plants recruit from saplings to the canopy. 2. We compared species and phylogenetic diversity of sapling and tree communities at two sites in French Guiana. We surveyed 2084 adult trees in four 1-ha tree plots and 943 saplings in sixteen 16-m2 subplots nested within the tree plots. Species diversity was measured using Fisher's alpha (species richness) and Simpson's index (species evenness). Phylogenetic diversity was measured using Faith's phylogenetic diversity (phylogenetic richness) and Rao's quadratic entropy index (phylogenetic evenness). The phylogenetic diversity indices were inferred using four phylogenetic hypotheses: two based on rbcLa plastid DNA sequences obtained from the inventoried individuals with different branch lengths, a global phylogeny available from the Angiosperm Phylogeny Group, and a combination of both. 3. Taxonomic identification of the saplings was performed by combining morphological and DNA barcoding techniques using three plant DNA barcodes (psbA-trnH, rpoC1 and rbcLa). DNA barcoding enabled us to increase species assignment and to assign unidentified saplings to molecular operational taxonomic units. 4. Species richness was similar between saplings and trees, but in about half of our comparisons, species evenness was higher in trees than in saplings. This suggests that negative density dependence plays an important role during the sapling-to-tree transition. 5. Phylogenetic richness increased between saplings and trees in about half of the comparisons. Phylogenetic evenness increased significantly between saplings and trees in a few cases (4 out of 16) and only with the most resolved phylogeny. These results suggest that negative density dependence operates largely independently of the phylogenetic structure of communities. 6. Synthesis. By contrasting species richness and evenness across size classes, we suggest that negative density dependence drives shifts in composition during the sapling-to-tree transition. In addition, we found little evidence for a change in phylogenetic diversity across age classes, suggesting that the observed patterns are not phylogenetically constrained.

A phylogenetic study of the subtribe Dicrepidiina (Elateridae, Elaterinae, Ampedini)

It is presented a cladistic analysis of the Dicrepidiina aiming to test the monophyletism of the subtribe and to establish the relationships among the genera. The subtribe is composed by 36 genera and all of them, except Asebis, Lamononia, Neopsephus, Semiotopsis and Spilomorphus were included in the analysis. Fifty two species, especially the type-species of each genus were studied: Achrestus flavocinctus (Candèze, 1859), A. venustus Champion, 1895, Adiaphorus gracilis Schwarz, 1901, A. ponticerianus Candèze, 1859, Anoplischiopsis bivittatus Champion, 1895, Anoplischius bicarinatus Candèze, 1859, A. conicus Candèze, 1900, A. haematopus Candèze, 1859, A. pyronotus Candèze, 1859, Atractosomus flavescens (Germar, 1839), Blauta cribraria (Germar, 1844), Calopsephus apicalis (Schwarz, 1903), Catalamprus angustus (Fleutiaux, 1902), Crepidius flabellifer (Erichson, 1847), C. resectus Candèze, 1859, Cyathodera auripilosus Costa, 1968, C. lanugicollis (Candèze, 1859), C. longicornis Blanchard, 1843, Dayakus angularis Candèze, 1893, Dicrepidius ramicornis (Palisot de Beauvois, 1805), Dipropus brasilianus (Germar, 1824), D. factuellus Candèze, 1859, D. laticollis (Eschscholtz, 1829), D. pinguis (Candèze, 1859), D. schwarzi (Becker, 1961), Elius birmanicus Candèze, 1893, E. dilatatus Candèze, 1878, Heterocrepidius gilvellus Candèze, 1859, H. ventralis Guérin-Méneville, 1838, Lampropsephus cyaneus (Candèze, 1878), Loboederus appendiculatus (Perty, 1830), Olophoeus gibbus Candèze, 1859, Ovipalpus pubescens Solier, 1851, Pantolamprus ligneus Candèze, 1896, P. mirabilis Candèze, 1896, P. perpulcher Westwood, 1842, Paraloboderus glaber Golbach, 1990, Proloboderus crassipes Fleutiaux, 1912, Propsephus beniensis (Candèze, 1859), P. cavifrons (Erichson, 1843), Pseudolophoeus guineensis (Candèze, 1881), Rhinopsephus apicalis (Schwarz, 1903), Sephilus formosanus Schwarz, 1912, S. frontalis Candèze, 1878, Singhalenus gibbus Candèze, 1892, S. taprobanicus Candèze, 1859, Sphenomerus antennalis Candèze, 1859, S. brunneus Candèze, 1865, Spilus atractomorphus Candèze, 1859, S. nitidus Candèze, 1859, Stenocrepidius simonii Fleutiaux, 1891 and Trielasmus varians Blanchard, 1846. Chalcolepidius zonatus (Hemirhipini, Agrypninae), Ctenicera silvatica (Prosternini, Prosterninae), and species of the other subtribes of Ampedini (Elaterinae): Ampedus sanguineus (Ampedina), Melanotus spernendus (Melanotina) and Anchastus digittatus and Physorhinus xanthocephalus (Physorhinina) were used as outgroups. The results of the phylogenetic analysis demonstrated that Dicrepidiina, as formerly defined, does not form a monophyletic group. One genus, represented by Ovipalpus pubescens, was removed from the subtribe. The subtribe is characterized by presence of lamella under 2nd and 3rd tarsomeres of all legs. Also, it was revealed that the genera Achrestus, Anoplischius, Dipropus and Propsephus are not monophyletic. Due to the scarcity of information, all the studied species are redescribed and illustrated.

Non-monophyly of the woody bamboos (Bambuseae; Poaceae): a multi-gene region phylogenetic analysis of Bambusoideae s.s.

The taxonomy of Bambusoideae is in a state of flux and phylogenetic studies are required to help resolve systematic issues. Over 60 taxa, representing all subtribes of Bambuseae and related non-bambusoid grasses were sampled. A combined analysis of five plastid DNA regions, trnL intron, trnL-F intergenic spacer, atpB-rbcL intergenic spacer, rps16 intron, and matK, was used to study the phylogenetic relationships among the bamboos in general and the woody bamboos in particular. Within the BEP clade (Bambusoideae s.s., Ehrhartoideae, Pooideae), Pooideae were resolved as sister to Bambusoideae s.s. Tribe Bambuseae, the woody bamboos, as currently recognized were not monophyletic because Olyreae, the herbaceous bamboos, were sister to tropical Bambuseae. Temperate Bambuseae were sister to the group consisting of tropical Bambuseae and Olyreae. Thus, the temperate Bambuseae would be better treated as their own tribe Arundinarieae than as a subgroup of Bambuseae. Within the tropical Bambuseae, neotropical Bambuseae were sister to the palaeotropical and Austral Bambuseae. In addition, Melocanninae were found to be sister to the remaining palaeotropical and Austral Bambuseae. We discuss phylogenetic and morphological patterns of diversification and interpret them in a biogeographic context.

Distributional patterns of the Neotropical genus Thecomyia Perty (Diptera, Sciomyzidae) and phylogenetic support

Distributional patterns of the Neotropical genus Thecomyia Perty (Diptera, Sciomyzidae) and phylogenetic support. The distributional pattern of the genus Thecomyia Perty, 1833 was defined using panbiogeographic tools, and analyzed based on the phylogeny of the group. This study sought to establish biogeographical homologies in the Neotropical region between different species of the genus, based on their distribution pattern and later corroboration through its phylogeny. Eight individual tracks and 16 generalized tracks were identified, established along nearly the entire swath of the Neotropics. Individual tracks are the basic units of a panbiogeographic study, and correspond to the hypothesis of minimum distribution of the organisms involved. The generalized tracks, obtained from the spatial congruence between two or more individual tracks, are important in the identification of smaller areas of endemism. Thus, we found evidence from the generalized tracks in support of previous classification for the Neotropical region. The Amazon domain is indicated as an area of outstanding importance in the diversification of the group, by the confluence of generalized tracks and biogeographic nodes in the region. Most of the generalized tracks and biogeographical nodes were congruent with the phylogenetic hypothesis of the genus, indicating support of the primary biogeographical homologies originally defined by the track analysis.

Do fly parasites of bats and their hosts coevolve?speciation in Trichobius phyllostomae group (Diptera, Streblidae) and their hosts (Chiroptera, Phyllostomidae) suggests that they do not

We examined whether, like many parasite-host systems of coevolution, a group of obligate parasitic bat flies (Trichobius phyllostomae Kessel and related species) cospeciate with their hosts. We first did a cladistic analysis of the T. phyllostomae group and combined that analysis with a phylogenetic hypothesis from the literature for the Stenodermatinae bats. The cladistic analysis included, as outgroups, one species from each morphological group and complex of Trichobius Gervais, and one species from the following genera: Paratrichobius Miranda-Ribeiro, Megistopoda Macquart, Megistapophysys Dick & Wenzel, Neotrichobius Wenzel & Aitken, Speiseria Kessel and Strebla Wiedemann. The cladogram was rooted with a species of Strebla in the subfamily Streblinae. One cladogram was obtained and which found Trichobius to be polyphyletic. The phylogenetic hypothesis as follows: (Paratrichobius, (Neotrichobius, (Megistopoda, Megistapophysis)))) is the sister-group of the phyllostomae group and the following relationships within the ingroup, (((T. vampyropis Wenzel, Trichobius sp. 2) ((T. hispidus Wenzel, T. petersoni Wenzel) ((Trichobius sp. 1 (T. phyllostomae, T. brennani Wenzel))))). When we compared phylogenies through historical association analyses, cospeciation was uncommon, while host-switching was more common and better explained the association between the phyllostomae group and their bat hosts.

Integrative taxonomy of the Formica rufa group (Hymenoptera: Formicidae)

RESUME :Les fourmis du groupe Formica rufa, ou fourmis des bois, ainsi appelées en raison de leur préférence pour les écosystèmes forestiers, sont parmi les fourmis les plus fascinantes et les plus étudiées d'Europe. Ces fourmis jouent un rôle clé dans la plupart des forêts dans lesquelles elles vivent et sont considérées comme étant les meilleurs bioindicateurs de ces milieux. Pour ces raisons, les fourmis des bois sont protégées par la loi dans de nombreux pays européens, y compris en Suisse. Cependant, malgré leur protection, ces fourmis sont inscrites sur la liste rouge des espèces menacées dans plusieurs pays d'Europe et il est donc indispensable de bien les connaître afin de mieux les protéger.À l'heure actuelle, on considère que le groupe Formica rufa est composé de six espèces distinctes : F. rufa, F. polyctena, F. lugubris, F. paralugubris, F. aquilonia et F. pratensis. Toutefois, malgré la grande quantité d'études effectuées sur ces espèces, la systématique et l'identification des fourmis des bois sont toujours sujettes à discussion. Ceci est essentiellement dû au fait que ces espèces sont morphologiquement similaires et qu'elles sont parfois capables de s'hybrider ou de former des colonies mixtes.Une des conditions fondamentales pour toute étude en biologie de la conservation est l'identification correcte des espèces à protéger. Avec cette étude, nous désirons donc dénouer les problèmes liés à la systématique des fourmis des bois et analyser la diversité de ces espèces en adoptant une approche multidisciplinaire.Nous avons d'abord étudié la distribution des espèces jumelles F. lugubris et F. paralugubris dans les Álpes italiennes en re-analysant l'une des plus grandes collections de références sur ces espèces, déposée à l'Université de Pavie, Italie, et en récoltant de nouveaux échantillons sur le terrain. Nos analyses ont montré que F, paralugubris, décrite récemment et souvent «oubliée »par les chercheurs, est bien présente dans les Alpes et vit souvent en sympathie avec F. lugubris. Ensuite nous avons développé un outil moléculaire basé sur l'ADN mitochondrial pour une identification rapide et efficace de ces deux espèces. Au vu des bons résultats, nous avons étendu nos analyses génétiques (microsatellites) à toutes les espèces du groupe F. rufa, ce qui nous a permis de montrer que les outils moléculaires sont très efficaces pour identifier ces fourmis. En outre, nos analyses ont mis en évidence la présence d'une nouvelle espèce cryptique (appelée F. lugubris-X) au sein du Parc National Suisse. L'existence d'une nouvelle espèce peut avoir une grande influence sur les projets de conservation en faveur de ces espèces. Nous avons donc décidé de confirmer ce résultat avec des analyses comportementales et des analyses chimiques basées sur les phéromones sexuelles des différentes espèces, y compris F. lugubris-X. Les deux approches confirment nos données génétiques et indiquent que F. lugubris-X représente bel et bien une nouvelle espèce de fourmis des bois dans les Alpes Suisses.Les résultats de cette étude ont une grande importance du point de vue de la biodiversité. En plus, ils livrent aux futurs chercheurs des outils fiables pour l'identification des fourmis des bois et ouvrent de captivantes perspectives pour une meilleure protection de ces insectes et, par conséquent, de nos écosystèmes forestiers. .Abstract :Mound building red wood ants (species of the Formica rufa group) belong to one of the most studied groups of ants in Europe and have fundamental roles and positive effects in forested habitats of the northern hemisphere. In addition, they are considered among the most promising bioindicators of forest ecosystems. Because of their importance, these ants are protected by law in many European countries, including Switzerland. However, despite this protection, they are included on the red list of threatened species edited by the International Union for Conservation of Nature (IUCN) and on the red list of some particular countries like Switzerland. Because of their similar morphology and a high intraspecific variability, the morphological identification of these species can be quite complicated. In addition, they are sometimes able to hybridize or to form mixed colonies. Consequently, the taxonomy of this group of ants has been much debated during the past decades. Based on a phylogenetic study, today the group is considered to count six species in Europe: F. rufa, F. po/yctena, F. lugubris, F. paralugubris, F. aquilonia and F. pratensis. Nevertheless, the taxonomy of the group is often neglected mainly due to the lack of reliable and easy to use identification methods.Considering the importance of correct species assessment in conservation biology, in this study we want to disentangle the taxonomical difficulties within the Formica rufa group and to clarify the diversity of these protected ants, by using an integrative approach.We first analyzed the distribution of .the sibling species F. lugubris and F. paralugubris in the Italian Alps by collecting new samples on the field and by examining one of the major red wood ant collections, which is deposited at the University of Pavia, Italy. After that, we developed a molecular tool based on mitochondria) DNA, which provides a reliable and easy-to-use technique for the identification of F. lugubris and F. paralugubris. Afterwards, we extended the use of molecular markers for species identification to the whole F. rufa group and made a microsatellite analysis. Results confirm that molecular markers are consistent tools for species identification and that the six known species represent six different genetic pools. In addition, genetic data highlighted the existence of a new cryptic species in the Swiss Alps, called Formica lugubris-X.The presence of a new species can have a great influence on future conservation plans in favour of these protected ants and consequently for forested habitats. We therefore completed molecular data by behavioural (pupae recognition) and chemical analyses based on six pheromones of the entire F. rufa group. Both approaches are in accordance to genetic results and confirm that F. lugubris-X really represents a new cryptic species of red wood ant within the Swiss National Park (Eastern Swiss Alps).Results obtained in this study have a great importance in terms of biodiversity. Moreover, they provide important taxonomical information, reliable tools for species identifications and future perspectives for a consequent conservation of red wood ant species.

Modeling the Emergence of Social Structure from a Phylogenetic Point of View

Based on provious (Hemelrijk 1998; Puga-González, Hildenbrant & Hemelrijk 2009), we have developed an agent-based model and software, called A-KinGDom, which allows us to simulate the emergence of the social structure in a group of non-human primates. The model includes dominance and affiliative interactions and incorporate s two main innovations (preliminary dominance interactions and a kinship factor), which allow us to define four different attack and affiliative strategies. In accordance with these strategies, we compared the data obtained under four simulation conditions with the results obtained in a provious study (Dolado & Beltran 2012) involving empirical observations of a captive group of mangabeys (Cercocebus torquatus)

Incidence of Garlic common latent virus in Argentina, and phylogenetic and recombination analyses of isolates

The objective of this work was to estimate the incidence and prevalence of Garlic common latent virus (GarCLV) in the main production regions of garlic (Allium sativum) in Argentina, and to perform phylogenetic and recombination analyses in isolates from these regions. Leaf samples (3,050) were taken from four garlic commercial types, in 13 departments of the four main garlic-producing provinces of Argentina, in a 1,175-ha sampling area. Virus infection was evaluated with DAS-Elisa test using specific antiserum, and the phylogenetic and recombination analyses were done with capsid protein (CP) nucleotide sequence of seven GarCLV isolates from the provinces. The incidence of GarCLV in the evaluated provinces varied between 6.7 and 22% of the samples, whereas the prevalence varied between 52.6 and 70%. In the analysis of garlic commercial types, Morado showed the highest incidence of the virus, in the province of San Juan, whereas Rosado Paraguayo had the lowest incidence, in the province of Cordoba. Nucleotide identity in the CP sequences ranged between 80.3 and 97.6%. The phylogenetic analysis shows the presence of two main groups of GarCLV and of a possible third group that would include only a German isolate. The recombination analysis between isolates from different parts of the world evidences the presence of recombinant isolates from Poland and Australia.

Methicillin-resistant Staphylococcus aureus: phylogenetic relatedness between European epidemic clones and Swiss sporadic strains.

We have compared the phylogenetic diversity of methicillin-resistant Staphylococcus aureus (MRSA) strains from Switzerland and their phylogenetic relationships with European epidemic clones, using multiprimer random amplification polymorphic DNA (RAPD). Strains included 24 European epidemic clones (59 strains), 66 sporadic strains isolated in Switzerland in 1996-1997, and 15 reference strains of five other Staphylococcus species. Similarity and clustering analysis with the Jaccard's coefficient showed that the maximum genetic distance between MRSA strains was 0.43, whereas the minimum genetic distance between the six Staphylococcus species was 0.97, indicating that the method permits phylogenetic hierarchization. The 24 MRSA clones reported to be epidemic in European countries during the 1990s were distributed into seven different genetic clusters with a maximum distance of 0.29 among them. This clustering pattern was confirmed by the analysis of a subset of MRSA strains by multilocus enzyme electrophoresis at 12 loci. Most of the sporadic Swiss strains were distributed into these seven different genetic clusters, together with the epidemic MRSA clones. This suggests that there is no phylogenetic cluster specific to epidemic clones of MRSA.