Aim Parrots are thought to have originated on Gondwana during the Cretaceous. The initial split within crown group parrots separated the New Zealand taxa from the remaining extant species and was considered to coincide with the separation of New Zealand from Gondwana 82-85 Ma, assuming that the diversification of parrots was mainly shaped by vicariance. However, the distribution patterns of several extant parrot groups cannot be explained without invoking transoceanic dispersal, challenging this assumption. Here, we present a temporal and spatial framework for the diversification of parrots using external avian fossils as calibration points in order to evaluate the relative importance of the influences of past climate change, plate tectonics and ecological opportunity.Location Australasian, African, Indo-Malayan and Neotropical regions.Methods Phylogenetic relationships were investigated using partial sequences of the nuclear genes c-mos, RAG-1 and Zenk of 75 parrot and 21 other avian taxa. Divergence dates and confidence intervals were estimated using a Bayesian relaxed molecular clock approach. Biogeographic patterns were evaluated taking temporal connectivity between areas into account. We tested whether diversification remained constant over time and if some parrot groups were more species-rich than expected given their age.Results Crown group diversification of parrots started only about 58 Ma, in the Palaeogene, significantly later than previously thought. The Australasian lories and possibly also the Neotropical Arini were found to be unexpectedly speciesrich. Diversification rates probably increased around the Eocene/Oligocene boundary and in the middle Miocene, during two periods of major global climatic aberrations characterized by global cooling.Main conclusions The diversification of parrots was shaped by climatic and geological events as well as by key innovations. Initial vicariance events caused by continental break-up were followed by transoceanic dispersal and local radiations. Habitat shifts caused by climate change and mountain orogenesis may have acted as a catalyst to the diversification by providing new ecological opportunities and challenges as well as by causing isolation as a result of habitat fragmentation. The lories constitute the only highly nectarivorous parrot clade, and their diet shift, associated with morphological innovation, may have acted as an evolutionary key innovation, allowing them to explore underutilized niches and promoting their diversification.

A series of 100 Staphylococcus aureus isolates ascribed to sequence type 398 (ST398) and recovered from different sources (healthy carrier and diseased pigs, dust from pig farms, milk, and meat) in Germany were investigated for their virulence and antimicrobial resistance genetic background. Antimicrobial resistance was determined by the disk diffusion method. Virulence and resistance determinants (37 and 31 genes, respectively) were tested by PCR. Only two virulence profiles, including the accessory gene regulator agrI and three or four hemolysin-encoding genes, were detected. In contrast, 33 resistance profiles were distinguished (only 11 were shown by more than one isolate). Fifty-nine isolates were multiresistant (four or more antimicrobial classes), and 98 were methicillin resistant (mecA positive). All of the ST398 isolates showed resistance to tetracycline [encoded by tet(M) alone or together with tet(K) and/or tet(L)]. In addition, 98% were resistant to other antimicrobials, including macrolide-lincosamine-streptogramin B (70%, encoded by ermA, ermB, and ermC, alone or in combination), trimethoprim (65%, mostly due to dfrK and dfrG), kanamycin and gentamicin [29% and 14%, respectively, mainly related to aac(6)-Ie-aph(2؆)-Ia and/or ant(4)-Ia but also to aph(3)-IIIa], chloramphenicol (9%, fexA or cfr), quinupristin-dalfopristin (9%), ciprofloxacin (8%), and trimethoprim-sulfamethoxazole (4%). The heterogeneity of the resistance profiles underlines the ability of the ST398 clone to acquire multiple antimicrobial resistance genes. However, the virulence gene content of the tested isolates was low. Continuous surveillance is needed to clarify whether its pathogenicity potential for animals and humans will increase over time.Methicillin-resistant Staphylococcus aureus (MRSA) of sequence type 398 (ST398) has gained particular attention during recent years because of its association with pigs and its ability to colonize pig farmers and other people in close contact with pigs (7,12,47). The MRSA isolates of ST398 usually lack important virulence determinants that are typical in other community and hospital MRSA isolates. The majority of the ST398 isolates analyzed so far carry only hemolysin-encoding genes (13,21,31,32), although a small number of cases in which the isolates carried the bicomponent leukotoxin PantonValentine (lukPV genes) (43, 49) or staphylococcal enterotoxins (SEs, se genes) (21, 26) have also been reported. Genes for other toxins, like exfoliatins (ET, et genes), leukotoxins, and toxic shock syndrome toxin (TSST-1, tst gene) have not been found yet in ST398 isolates (13,21,31,32,44). The regulation of the expression of most extracellular virulence factors in S. aureus is under the control of a two-component signaling system called the accessory gene regulator (agr), which is polymorphic and divided into four distinct genetic groups (I to IV). A correlation exists between some agr groups and certain pathotypes and clonal complexes (CCs) (48), and CC398 seem to be associated with agr group I (ag...

ABSTRACTIn 2011, Germany experienced the largest outbreak with a Shiga toxin-producingEscherichia coli(STEC) strain ever recorded. A series of environmental and trace-back and trace-forward investigations linked sprout consumption with the disease, but fecal-oral transmission was also documented. The genome sequences of the pathogen revealed a clonal outbreak with enteroaggregativeE. coli(EAEC). Some EAEC virulence factors are carried on the virulence plasmid pAA. From an unknown source, the epidemic strains acquired a lambdoid prophage carrying the gene for the Shiga toxin. The resulting strains therefore possess two different mobile elements, a phage and a plasmid, contributing essential virulence genes. Shiga toxin is released by decaying bacteria in the gut, migrates through the intestinal barrier, and is transported via the blood to target organs, like the kidney. In a mouse model, probiotic bifidobacteria interfered with transport of the toxin through the gut mucosa. Researchers explored bacteriophages, bacteriocins, and low-molecular-weight inhibitors against STEC. Randomized controlled clinical trials of enterohemorrhagicE. coli(EHEC)-associated hemolytic uremic syndrome (HUS) patients found none of the interventions superior to supportive therapy alone. Antibodies against one subtype of Shiga toxin protected pigs against fatal neurological infection, while treatment with a toxin receptor decoy showed no effect in a clinical trial. Likewise, a monoclonal antibody directed against a complement protein led to mixed results. Plasma exchange and IgG immunoadsoprtion ameliorated the condition in small uncontrolled trials. The epidemic O104:H4 strains were resistant to all penicillins and cephalosporins but susceptible to carbapenems, which were recommended for treatment.

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A specific PCR for the detection of a variant of the gene encoding Shiga toxin 1 (stx 1 ) called stx 1 OX3 (GenBank accession no. Z36901) was developed. The PCR was used to investigate 148 Stx 1 -producing Escherichia coli strains from human patients (n ‫؍‬ 72), cattle (n ‫؍‬ 27), sheep (n ‫؍‬ 48), and a goat (n ‫؍‬ 1) for the presence of the stx 1 OX3 gene. The stx 1 OX3 gene was present in 38 Shiga toxin-producing E. coli (STEC) strains from sheep belonging to serogroups O5, O125, O128, O146, and OX3 but was absent from Stx 1 -positive ovine STEC O91 strains. The stx 1 OX3 gene was also detected in 22 STEC strains from humans with nonbloody diarrhea and from asymptomatic excreters. Serotypes O146:H21 and O128:H2 were most frequently associated with stx 1 OX3 -carrying STEC from sheep and humans. In contrast, Stx 1 -producing STEC strains from cattle and goats and 50 STEC strains from humans were all negative for the stx 1 OX3 gene. The stx 1 OX3 -negative strains belonged to 13 serotypes which were different from those of the stx 1 OX3 -positive STEC strains. Moreover, the stx 1 OX3 gene was not associated with STEC belonging to enterohemorrhagic E. coli (EHEC) serogroups O26, O103, O111, O118, O145, and O157. A bacteriophage carrying the stx 1 OX3 gene (phage 6220) was isolated from a human STEC O146:H21 strain. The phage was able to lysogenize laboratory E. coli K-12 strain C600. Phage 6220 shared a similar morphology and a high degree of DNA homology with Stx 2 -encoding phage 933W, which originates from EHEC O157. In contrast, few similarities were found between phage 6220 and Stx 1 -encoding bacteriophage H-19B from EHEC O26.The production of Shiga toxins (verocytotoxins) Stx1 and Stx2 is associated with certain strains of Escherichia coli. Ruminant animals such as cattle, sheep, and goats are naturally colonized with Shiga-toxin-producing strains of E. coli (STEC) and shed these organisms with their feces into the environment. Humans can be infected with STEC by contaminated food and by direct transmission of bacteria, and some STEC types pathogenic for humans cause diarrhea, hemorrhagic colitis, and hemolytic-uremic syndrome (16). Over 200 serotypes of E. coli are known to be associated with the production of Shiga toxins (16). Analysis of the genes encoding Stx1 and Stx2 revealed the existence of various stx subtypes which show differences in their nucleotide sequences. In some strains, the stx genes were found to be carried by temperate bacteriophages, such as stx 1 in STEC O26 and stx 1 and stx 2 in STEC O157 (12,18,20,32,34). A variant of the stx gene of Shigella sonnei and a variant of the stx 2e gene, which is present in porcine STEC strains, were recently found to be carried by bacteriophages (7,15). On the other hand, the stx gene of Shigella dysenteriae type 1 and some other variants of stx 1 and stx 2 present in E. coli were not associated with viable bacteriophages (11,23,35).Paton et al. have described four variants of the stx 1 gene in STEC strains isolated from humans and animals (22, 24)....

BackgroundAnimal faeces comprise a community of many different microorganisms including bacteria and viruses. Only scarce information is available about the diversity of viruses present in the faeces of pigs. Here we describe a protocol, which was optimized for the purification of the total fraction of viral particles from pig faeces. The genomes of the purified DNA and RNA viruses were simultaneously amplified by PCR and subjected to deep sequencing followed by bioinformatic analyses. The efficiency of the method was monitored using a process control consisting of three bacteriophages (T4, M13 and MS2) with different morphology and genome types. Defined amounts of the bacteriophages were added to the sample and their abundance was assessed by quantitative PCR during the preparation procedure.ResultsThe procedure was applied to a pooled faecal sample of five pigs. From this sample, 69,613 sequence reads were generated. All of the added bacteriophages were identified by sequence analysis of the reads. In total, 7.7% of the reads showed significant sequence identities with published viral sequences. They mainly originated from bacteriophages (73.9%) and mammalian viruses (23.9%); 0.8% of the sequences showed identities to plant viruses. The most abundant detected porcine viruses were kobuvirus, rotavirus C, astrovirus, enterovirus B, sapovirus and picobirnavirus. In addition, sequences with identities to the chimpanzee stool-associated circular ssDNA virus were identified. Whole genome analysis indicates that this virus, tentatively designated as pig stool-associated circular ssDNA virus (PigSCV), represents a novel pig virus.ConclusionThe established protocol enables the simultaneous detection of DNA and RNA viruses in pig faeces including the identification of so far unknown viruses. It may be applied in studies investigating aetiology, epidemiology and ecology of diseases. The implemented process control serves as quality control, ensures comparability of the method and may be used for further method optimization.

The grey wolf (Canis lupus) was the first species to give rise to a domestic population, and they remained widespread throughout the last Ice Age when many other large mammal species went extinct. Little is known, however, about the history and possible extinction of past wolf populations or when and where the wolf progenitors of the present-day dog lineage (Canis familiaris) lived1–8. Here we analysed 72 ancient wolf genomes spanning the last 100,000 years from Europe, Siberia and North America. We found that wolf populations were highly connected throughout the Late Pleistocene, with levels of differentiation an order of magnitude lower than they are today. This population connectivity allowed us to detect natural selection across the time series, including rapid fixation of mutations in the gene IFT88 40,000–30,000 years ago. We show that dogs are overall more closely related to ancient wolves from eastern Eurasia than to those from western Eurasia, suggesting a domestication process in the east. However, we also found that dogs in the Near East and Africa derive up to half of their ancestry from a distinct population related to modern southwest Eurasian wolves, reflecting either an independent domestication process or admixture from local wolves. None of the analysed ancient wolf genomes is a direct match for either of these dog ancestries, meaning that the exact progenitor populations remain to be located.