Multidrug-Resistant Staphylococcus aureus in US Meat and Poultry

We characterized the prevalence, antibiotic susceptibility profiles, and genotypes of Staphylococcus aureus among US meat and poultry samples (n = 136). S. aureus contaminated 47% of samples, and multidrug resistance was common among isolates (52%). S. aureus genotypes and resistance profiles differed significantly among sample types, suggesting food animal–specific contamination.

Interactions between the yeast Ogataea pini and filamentous fungi associated with the western pine beetle

Ecologically important microbes other than filamentous fungi can be housed within the fungal-transport structures (mycangia) of Dendroctonus bark beetles. The yeast Ogataea pini (Saccharomycetales: Saccharomycetaceae) was isolated from the mycangia of western pine beetle (Dendroctonus brevicomis) populations in northern Arizona (USA) with a frequency of 56%. We performed a series of in vitro assays to test whether volatile organic compounds produced by O. pini affected radial growth rates of mutualistic and antagonistic species of filamentous fungi that are commonly found in association with the beetle including Entomocorticium sp. B, Ophiostoma minus, Beauvaria bassiana, and an Aspergillus sp. We determined the compounds O. pini produced when grown on 2% malt extract agar using a gas chromatography/mass spectrometry (GC/MS) analysis of headspace volatiles. Volatiles produced by O. pini on artificial media significantly enhanced the growth of the mutualistic Entomocorticium sp. B, and inhibited growth of the entomopathogenic fungus B. bassiana. GC/MS revealed that O. pini produced ethanol, carbon disulfide (CS(2)), and Δ-3-carene in headspace. The results of these studies implicate O. pini as an important component in D. brevicomis community ecology, and we introduce multiple hypotheses for future tests of the effects of yeasts in the symbiont assemblages associated with Dendroctonus bark beetles.

Single nucleotide polymorphisms for assessing genetic diversity in castor bean (Ricinus communis)

BACKGROUND

Castor bean (Ricinus communis) is an agricultural crop and garden ornamental that is widely cultivated and has been introduced worldwide. Understanding population structure and the distribution of castor bean cultivars has been challenging because of limited genetic variability. We analyzed the population genetics of R. communis in a worldwide collection of plants from germplasm and from naturalized populations in Florida, U.S. To assess genetic diversity we conducted survey sequencing of the genomes of seven diverse cultivars and compared the data to a reference genome assembly of a widespread cultivar (Hale). We determined the population genetic structure of 676 samples using single nucleotide polymorphisms (SNPs) at 48 loci.

RESULTS

Bayesian clustering indicated five main groups worldwide and a repeated pattern of mixed genotypes in most countries. High levels of population differentiation occurred between most populations but this structure was not geographically based. Most molecular variance occurred within populations (74%) followed by 22% among populations, and 4% among continents. Samples from naturalized populations in Florida indicated significant population structuring consistent with local demes. There was significant population differentiation for 56 of 78 comparisons in Florida (pairwise population phiPT values, p < 0.01).

CONCLUSION

Low levels of genetic diversity and mixing of genotypes have led to minimal geographic structuring of castor bean populations worldwide. Relatively few lineages occur and these are widely distributed. Our approach of determining population genetic structure using SNPs from genome-wide comparisons constitutes a framework for high-throughput analyses of genetic diversity in plants, particularly in species with limited genetic diversity.

Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer

Background

Phylogeographic reconstruction of some bacterial populations is hindered by low diversity coupled with high levels of lateral gene transfer. A comparison of recombination levels and diversity at seven housekeeping genes for eleven bacterial species, most of which are commonly cited as having high levels of lateral gene transfer shows that the relative contributions of homologous recombination versus mutation for Burkholderia pseudomallei is over two times higher than for Streptococcus pneumoniae and is thus the highest value yet reported in bacteria. Despite the potential for homologous recombination to increase diversity, B. pseudomallei exhibits a relative lack of diversity at these loci. In these situations, whole genome genotyping of orthologous shared single nucleotide polymorphism loci, discovered using next generation sequencing technologies, can provide very large data sets capable of estimating core phylogenetic relationships. We compared and searched 43 whole genome sequences of B. pseudomallei and its closest relatives for single nucleotide polymorphisms in orthologous shared regions to use in phylogenetic reconstruction.

Results

Bayesian phylogenetic analyses of >14,000 single nucleotide polymorphisms yielded completely resolved trees for these 43 strains with high levels of statistical support. These results enable a better understanding of a separate analysis of population differentiation among >1,700 B. pseudomallei isolates as defined by sequence data from seven housekeeping genes. We analyzed this larger data set for population structure and allele sharing that can be attributed to lateral gene transfer. Our results suggest that despite an almost panmictic population, we can detect two distinct populations of B. pseudomallei that conform to biogeographic patterns found in many plant and animal species. That is, separation along Wallace's Line, a biogeographic boundary between Southeast Asia and Australia.

Conclusion

We describe an Australian origin for B. pseudomallei, characterized by a single introduction event into Southeast Asia during a recent glacial period, and variable levels of lateral gene transfer within populations. These patterns provide insights into mechanisms of genetic diversification in B. pseudomallei and its closest relatives, and provide a framework for integrating the traditionally separate fields of population genetics and phylogenetics for other bacterial species with high levels of lateral gene transfer.

Phylogenetic understanding of clonal populations in an era of whole genome sequencing

Phylogenetic hypotheses using whole genome sequences have the potential for unprecedented accuracy, yet a failure to understand issues associated with discovery bias, character sampling, and strain sampling can lead to highly erroneous conclusions. For microbial pathogens, phylogenies derived from whole genome sequences are becoming more common, as large numbers of characters distributed across entire genomes can yield extremely accurate phylogenies, particularly for strictly clonal populations. The availability of whole genomes is increasing as new sequencing technologies reduce the cost and time required for genome sequencing. Until entire sample collections can be fully sequenced, harnessing the phylogenetic power from whole genome sequences in more than a small subset of fully sequenced strains requires the integration of whole genome and partial genome genotyping data. Such integration involves discovering evolutionarily stable polymorphic characters by whole genome comparisons, then determining allelic states across a wide panel of isolates using high-throughput genotyping technologies. Here, we demonstrate how such an approach using single nucleotide polymorphisms (SNPs) yields highly accurate, but biased phylogenetic reconstructions and how the accuracy of the resulting tree is compromised by incomplete taxon and character sampling. Despite recent phylogenetic work detailing the strengths and biases of integrating whole genome and partial genome genotype data, these issues are relatively new and remain poorly understood by many researchers. Here, we revisit these biases and provide strategies for maximizing phylogenetic accuracy. Although we write this review with bacterial pathogens in mind, these concepts apply to any clonally reproducing population or indeed to any evolutionarily stable marker that is inherited in a strictly clonal manner. Understanding the ways in which current and emerging technologies can be used to maximize phylogenetic knowledge is advantageous only with a complete understanding of the strengths and weaknesses of these methods.

Whole-genome-based phylogeny and divergence of the genus Brucella

Brucellae are worldwide bacterial pathogens of livestock and wildlife, but phylogenetic reconstructions have been challenging due to limited genetic diversity. We assessed the taxonomic and evolutionary relationships of five Brucella species-Brucella abortus, B. melitensis, B. suis, B. canis, and B. ovis-using whole-genome comparisons. We developed a phylogeny using single nucleotide polymorphisms (SNPs) from 13 genomes and rooted the tree using the closely related soil bacterium and opportunistic human pathogen, Ochrobactrum anthropi. Whole-genome sequencing and a SNP-based approach provided the requisite level of genetic detail to resolve species in the highly conserved brucellae. Comparisons among the Brucella genomes revealed 20,154 orthologous SNPs that were shared in all genomes. Rooting with Ochrobactrum anthropi reveals that the B. ovis lineage is basal to the rest of the Brucella lineage. We found that B. suis is a highly divergent clade with extensive intraspecific genetic diversity. Furthermore, B. suis was determined to be paraphyletic in our analyses, only forming a monophyletic clade when the B. canis genome was included. Using a molecular clock with these data suggests that most Brucella species diverged from their common B. ovis ancestor in the past 86,000 to 296,000 years, which precedes the domestication of their livestock hosts. Detailed knowledge of the Brucella phylogeny will lead to an improved understanding of the ecology, evolutionary history, and host relationships for this genus and can be used for determining appropriate genotyping approaches for rapid detection and diagnostic assays for molecular epidemiological and clinical studies.

Pre-Columbian origins for North American anthrax

Disease introduction into the New World during colonial expansion is well documented and had a major impact on indigenous populations; however, few diseases have been associated with early human migrations into North America. During the late Pleistocene epoch, Asia and North America were joined by the Beringian Steppe ecosystem which allowed animals and humans to freely cross what would become a water barrier in the Holocene. Anthrax has clearly been shown to be dispersed by human commerce and trade in animal products contaminated with Bacillus anthracis spores. Humans appear to have brought B. anthracis to this area from Asia and then moved it further south as an ice-free corridor opened in central Canada approximately 13,000 ybp. In this study, we have defined the evolutionary history of Western North American (WNA) anthrax using 2,850 single nucleotide polymorphisms (SNPs) and 285 geographically diverse B. anthracis isolates. Phylogeography of the major WNA B. anthracis clone reveals ancestral populations in northern Canada with progressively derived populations to the south; the most recent ancestor of this clonal lineage is in Eurasia. Our phylogeographic patterns are consistent with B. anthracis arriving with humans via the Bering Land Bridge. This northern-origin hypothesis is highly consistent with our phylogeographic patterns and rates of SNP accumulation observed in current day B. anthracis isolates. Continent-wide dispersal of WNA B. anthracis likely required movement by later European colonizers, but the continent's first inhabitants may have seeded the initial North American populations.

Convergent evolution of 'creepers' in the Hawaiian honeycreeper radiation

Natural selection plays a fundamental role in the ecological theory of adaptive radiation. A prediction of this theory is the convergent evolution of traits in lineages experiencing similar environments. The Hawaiian honeycreepers are a spectacular example of adaptive radiation and may demonstrate convergence, but uncertainty about phylogenetic relationships within the group has made it difficult to assess such evolutionary patterns. We examine the phylogenetic relationships of the Hawaii creeper (Oreomystis mana), a bird that in a suite of morphological, ecological and behavioural traits closely resembles the Kauai creeper (Oreomystis bairdi), but whose mitochondrial DNA (mtDNA) and osteology suggest a relationship with the amakihis (Hemignathus in part) and akepas (Loxops). We analysed nuclear DNA sequence data from 11 relevant honeycreeper taxa and one outgroup to test whether the character contradiction results from historical hybridization and mtDNA introgression, or convergent evolution. We found no evidence of past hybridization, a phenomenon that remains undocumented in Hawaiian honeycreepers, and confirmed mtDNA and osteological evidence that the Hawaii creeper is most closely related to the amakihis and akepas. Thus, the morphological, ecological and behavioural similarities between the evolutionarily distant Hawaii and Kauai creepers represent an extreme example of convergent evolution and demonstrate how natural selection can lead to repeatable evolutionary outcomes.

Introduced birds and the fate of hawaiian rainforests

The Hawaiian Islands have lost nearly all their native seed dispersers, but have gained many frugivorous birds and fleshy-fruited plants through introductions. Introduced birds may not only aid invasions of exotic plants but also may be the sole dispersers of native plants. We assessed seed dispersal at the ecotone between native- and exotic-dominated forests and quantified bird diets, seed rain from defecated seeds, and plant distributions. Introduced birds were the primary dispersers of native seeds into exotic-dominated forests, which may have enabled six native understory plant species to become reestablished. Some native plant species are now as common in exotic forest understory as they are in native forest. Introduced birds also dispersed seeds of two exotic plants into native forest, but dispersal was localized or establishment minimal. Seed rain of bird-dispersed seeds was extensive in both forests, totaling 724 seeds of 9 native species and 2 exotics with over 85% of the seeds coming from native plants. Without suitable native dispersers, most common understory plants in Hawaiian rainforests now depend on introduced birds for dispersal, and these introduced species may actually facilitate perpetuation, and perhaps in some cases restoration, of native forests. We emphasize, however, that restoration of native forests by seed dispersal from introduced birds, as seen in this study, depends on the existence of native forests to provide a source of seeds and protection from the effects of ungulates. Our results further suggest that aggressive control of patches of non-native plants within otherwise native-dominated forests may be an important and effective conservation strategy.

Prostaglandin production by amnion and decidual cells in response to bacterial products

Media from bacterial cultures have been tested for actions on prostaglandin biosynthesis by human amnion and decidual cells. The bacterial species, which are commonly associated with intrauterine infections, were Group B streptococcus, Escherichia coli, Fusobacterium nucleatum, Bacteroides fragilis, Gardnerella vaginalis, Neisseria gonorrhea, Mycoplasma hominis and Ureaplasma urealyticum. Overall, low doses of bacterial products were stimulatory of amnion prostaglandin production, whereas high doses were inhibitory. A similar pattern of results was obtained for effects on decidual prostaglandin production, although stimulatory actions at low doses were less pronounced. In all experiments interleukin 1 beta consistently induced a stimulation of prostaglandin production that greatly exceeded that caused by any bacterial product. It is possible that the inhibitory action of high doses of bacterial products on prostaglandin biosynthesis may contribute to the poor course of labor experienced by women with chorioamnionitis. Furthermore, these data lend credence to the view that the host response to infection (i.e. cytokine secretion) is the major mediator of subsequent preterm labor.

Hospitals in the year 2000: a scenario

Hospitals came into the twentieth century as creations of local, usually altruistic, interests and wrestled with accelerating change throughout the decades. Their success brought third-party financing, employee health plans, and government guarantees for charity care. Success seemed to breed success, and they raced ahead with capital investment in bricks, mortar, and high technology, only to find themselves in increasing trouble as 1990 approached. Writing from the precarious perch of the year 2000, the author views the worsening hospital situation and raises questions about the contradictions of federal interventions, the efforts to create "systems," the plight of small hospitals, and the love-hate role of medical staffs. Offered for consideration is a scenario of a health care crisis in the early 1990s comparable to the savings and loan crisis of 1988. However, this time the federal intervention is not simply in dollars, but, instead, brings on a "health for all" program with national financing and decentralized "district health" management. As in other nations of the world, hospitals become an integral part of the commitment to attack the root causes of ill health.

Cost containment: are hospitals taking a bum rap?

The private market has been distorted by government regulations and programs; more reliance on market incentives rather than on regulation is needed.