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Background: Methicillin-resistant Staphylococcus aureus (MRSA) is one of the most common healthcare-associated pathogens. To examine the role of inter-hospital patient sharing on MRSA transmission, a previous study collected 2,214 samples from 30 hospitals in Orange County, California and showed by spa typing that genetic differentiation decreased significantly with increased patient sharing. In the current study, we focused on the 986 samples with spa type t008 from the same population. Methods: We used genome sequencing to determine the effect of patient sharing on genetic differentiation between hospitals. Genetic differentiation was measured by between-hospital genetic diversity, FST, and the proportion of nearly identical isolates between hospitals. Results: Surprisingly, we found very similar genetic diversity within and between hospitals, and no significant association between patient sharing and genetic differentiation measured by FST. However, in contrast to FST, there was a significant association between patient sharing and the proportion of nearly identical isolates between hospitals. We propose that the proportion of nearly identical isolates is more powerful at determining transmission dynamics than traditional estimators of genetic differentiation (FST) when gene flow between populations is high, since it is more responsive to recent transmission events. Our hypothesis was supported by the results from coalescent simulations. Conclusions: Our results suggested that there was a high level of gene flow between hospitals facilitated by patient sharing, and that the proportion of nearly identical isolates is more sensitive to population structure than FST when gene flow is high. [ABSTRACT FROM AUTHOR]

During the last 2 decades, community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) strains have dramatically increased the global burden of S. aureus infections. The pandemic sequence type (ST)8/pulsed-field gel type USA300 is the dominant CA-MRSA clone in the United States, but its evolutionary history and basis for biological success are incompletely understood. Here, we use whole-genome sequencing of 387 ST8 isolates drawn from an epidemiological network of CA-MRSA infections and colonizations in northern Manhattan to explore short-term evolution and transmission patterns. Phylogenetic analysis predicted that USA300 diverged from a most common recent ancestor around 1993. We found evidence for multiple introductions of USA300 and reconstructed the phylogeographic spread of isolates across neighborhoods. Using pair-wise single-nucleotide polymorphism distances as a measure of genetic relatedness between isolates, we observed that most USA300 isolates had become endemic in households, indicating their critical role as reservoirs for transmission and diversification. Using the maximum single-nucleotide polymorphism variability of isolates from within households as a threshold, we identified several possible transmission networks beyond households. Our study also revealed the evolution of a fluoroquinolone-resistant subpopulation in the mid-1990s and its subsequent expansion at a time of high-frequency outpatient antibiotic use. This high-resolution phylogenetic analysis of ST8 has documented the genomic changes associated with USA300 evolution and how some of its recent evolution has been shaped by antibiotic use. By integrating whole-genome sequencing with detailed epidemiological analyses, our study provides an important framework for delineating the full diversity and spread of USA300 and other emerging pathogens in large urban community populations. [ABSTRACT FROM AUTHOR]

The phylogenetic position of Sipuncula, a group of unsegmented marine worms, has been controversial for several decades: Especially based on morphological data, closer relationships to Mollusca or Annelida were among the most favoured hypotheses. Increasing amounts of molecular data in recent years have consistently placed Sipuncula either in close affinity to or even within Annelida, the segmented worms, and rejected a close relationship to Mollusca. Yet, it remained uncertain whether Sipuncula is the sister group of Annelida or an annelid subtaxon. Therefore, herein we gathered data for five nuclear genes, which have been rarely used regarding Annelida and Sipuncula, and combined these with data for six previously used genes to further elucidate the phylogenetic position of Sipuncula. We also compiled a data set for 78 ribosomal proteins from publicly available genomic data sets. These are the two largest data sets for annelids with more than 10 taxa to date. All analyses placed Sipuncula within Annelida. For the first time, topology tests significantly rejected the possibility that Sipuncula is sister to Annelida. Thus, our analyses revealed that Sipuncula had secondarily lost segmentation. Given that unsegmented Echiura is also an annelid subtaxon, segmentation, a key character of Annelida, is much more variable than previously thought. Yet, this conclusion does not support the hypothesis that the last common ancestor of Annelida, Arthropoda and Chordata was segmented, assuming several losses along the branches leading to them. As yet no traces of segmentation could be shown in taxa exhibiting serially organized organ systems such as certain Mollusca, while in Sipuncula and Echiura such traces could be demonstrated. An independent origin of segmentation in Annelida, Arthropoda and Chordata thus appears to be more plausible and parsimonious. [ABSTRACT FROM AUTHOR]

Due to the lack of fossil evidence, the timescales of bacterial evolution are largely unknown. The speed with which genetic change accumulates in populations of pathogenic bacteria, however, is a key parameter that is crucial for understanding the emergence of traits such as increased virulence or antibiotic resistance, together with the forces driving pathogen spread. Methicillin-resistant Staphylococcus aureus (MRSA) is a common cause of hospital-acquired infections. We have investigated an MRSA strain (ST225) that is highly prevalent in hospitals in Central Europe. By using mutation discovery at 269 genetic loci (118,804 basepairs) within an international isolate collection, we ascertained extremely low diversity among European ST225 isolates, indicating that a recent population bottleneck had preceded the expansion of this clone. In contrast, US isolates were more divergent, suggesting they represent the ancestral population. While diversity was low, however, our results demonstrate that the short-term evolutionary rate in this natural population of MRSA resulted in the accumulation of measurable DNA sequence variation within two decades, which we could exploit to reconstruct its recent demographic history and the spatiotemporal dynamics of spread. By applying Bayesian coalescent methods on DNA sequences serially sampled through time, we estimated that ST225 had diverged since approximately 1990 (1987 to 1994), and that expansion of the European clade began in 1995 (1991 to 1999), several years before the new clone was recognized. Demographic analysis based on DNA sequence variation indicated a sharp increase of bacterial population size from 2001 to 2004, which is concordant with the reported prevalence of this strain in several European countries. A detailed ancestry-based reconstruction of the spatiotemporal dispersal dynamics suggested a pattern of frequent transmission of the ST225 clone among hospitals within Central Europe. In addition, comparative genomics indicated complex bacteriophage dynamics. [ABSTRACT FROM AUTHOR]

Abstract: A phylogeny for 29 species of scincine lizards from Madagascar, based on 3693 bp of six mitochondrial and five nuclear genes, revealed multiple parallel evolution of adaptations for a burrowing life, and unexpected relationships of the monotypic genera Androngo and Cryptoscincus. Androngo trivittatus was sister to Pygomeles braconnieri, and Cryptoscincus minimus was deeply nested within the genus Paracontias, all of these being fossorial taxa of elongated bodies and partly or fully reduced limbs. To account for these results, we place Cryptoscincus as a junior synonym of Paracontias, and discuss possible taxonomic consequences that may affect the status of Androngo, once additional data become available. [Copyright &y& Elsevier]

The article discusses a study which examines the evolution of pathogens using the ancient bacterial DNA and changes on human health. It found that yersinia pestis was responsibble for the Black Deaths during the 14th-17th centuries and modern pandemic in the 19th-20th centuries. It also adds the evolution of pathogens by comparing the ancient and presents genomes.

Hospital-associated methicillin-resistant Staphylococcus aureus (MRSA) infections are frequently caused by predominant clusters of closely related isolates that cannot be discriminated by conventional diagnostic typing methods. Whole genome sequencing (WGS) and DNA microarray (MA) now allow for better discrimination within a prevalent clonal complex (CC). This single center exploratory study aims to distinguish invasive (blood stream infection) and non-invasive (nasal colonization) MRSA isolates of the same CC5 into phylogenetic- and virulence-associated genotypic subgroups by WGS and MA. A cohort of twelve blood stream and fifteen nasal MRSA isolates of CC5 ( spa -types t003 and t504 ) was selected. Isolates were propagated at the same period of time from unrelated patients treated at the University of Saarland Medical Center, Germany. Rooted phylotyping based on WGS with core-genome single nucleotide polymorphism (SNP) analysis revealed two local clusters of closely related CC5 subgroups ( t504 and Clade1 t003 ) which were separated from other local t003 isolates and from unrelated CC5 MRSA reference isolates of German origin. Phylogenetic subtyping was not associated with invasiveness when comparing blood stream and nasal isolates. Clustering based on MA profiles was not concordant with WGS phylotyping, but MA profiles may identify subgroups of isolates with nasal and blood stream origin. Among the new putative virulence associated genes identified by WGS, the strongest association with blood stream infections was shown for ebh B mutants. Analysis of the core-genome together with the accessory genome enables subtyping of closely related MRSA isolates according to phylogeny and presumably also to the potential virulence capacity of isolates. [ABSTRACT FROM AUTHOR]

Bacterial virulence is a multifaceted trait where the interactions between pathogen and host factors affect the severity and outcome of the infection. Toxin secretion is central to the biology of many bacterial pathogens and is widely accepted as playing a crucial role in disease pathology. To understand the relationship between toxicity and bacterial virulence in greater depth, we studied two sequenced collections of the major human pathogen Staphylococcus aureus and found an unexpected inverse correlation between bacterial toxicity and disease severity. By applying a functional genomics approach, we identified several novel toxicity-affecting loci responsible for the wide range in toxic phenotypes observed within these collections. To understand the apparent higher propensity of low toxicity isolates to cause bacteraemia, we performed several functional assays, and our findings suggest that within-host fitness differences between high- and low-toxicity isolates in human serum is a contributing factor. As invasive infections, such as bacteraemia, limit the opportunities for onward transmission, highly toxic strains could gain an additional between-host fitness advantage, potentially contributing to the maintenance of toxicity at the population level. Our results clearly demonstrate how evolutionary trade-offs between toxicity, relative fitness, and transmissibility are critical for understanding the multifaceted nature of bacterial virulence. [ABSTRACT FROM AUTHOR]

Summary: Background: The emergence of Neisseria gonorrhoeae with decreased susceptibility to extended spectrum cephalosporins raises the prospect of untreatable gonorrhoea. In the absence of new treatments, efforts to slow the increasing incidence of resistant gonococcus require insight into the factors that contribute to its emergence and spread. We assessed the relatedness between isolates in the USA and reconstructed likely spread of lineages through different sexual networks. Methods: We sequenced the genomes of 236 isolates of N gonorrhoeae collected by the Centers for Disease Control and Prevention's Gonococcal Isolate Surveillance Project (GISP) from sentinel public sexually transmitted disease clinics in the USA, including 118 (97%) of the isolates from 2009–10 in GISP with reduced susceptibility to cefixime (cefRS) and 118 cefixime-susceptible isolates from GISP matched as closely as possible by location, collection date, and sexual orientation. We assessed the association between antimicrobial resistance genotype and phenotype and correlated phylogenetic clustering with location and sexual orientation. Findings: Mosaic penA XXXIV had a high positive predictive value for cefRS. We found that two of the 118 cefRS isolates lacked a mosaic penA allele, and rechecking showed that these two were susceptible to cefixime. Of the 116 remaining cefRS isolates, 114 (98%) fell into two distinct lineages that have independently acquired mosaic penA allele XXXIV. A major lineage of cefRS strains spread eastward, predominantly through a sexual network of men who have sex with men. Eight of nine inferred transitions between sexual networks were introductions from men who have sex with men into the heterosexual population. Interpretation: Genomic methods might aid efforts to slow the spread of antibiotic-resistant N gonorrhoeae through augmentation of gonococcal outbreak surveillance and identification of populations that could benefit from increased screening for aymptomatic infections. Funding: American Sexually Transmitted Disease Association, Wellcome Trust, National Institute of General Medical Sciences, and National Institute of Allergy and Infectious Diseases, National Institutes of Health. [ABSTRACT FROM AUTHOR]

Streptococcus pneumoniae of serotype 3 possess a mucoid capsule and cause disease associated with high mortality rates relative to other pneumococci. Phylogenetic analysis of a complete reference genome and 81 draft sequences from clonal complex 180, the predominant serotype 3 clone in much of the world, found most sampled isolates belonged to a clade affected by few diversifying recombinations. However, other isolates indicate significant genetic variation has accumulated over the clonal complex's entire history. Two closely related genomes, one from the blood and another from the cerebrospinal fluid, were obtained from a patient with meningitis. The pair differed in their behaviour in a mouse model of disease and in their susceptibility to antimicrobials, with at least some of these changes attributable to a mutation that up-regulated the patAB efflux pump. This indicates clinically important phenotypic variation can accumulate rapidly through small alterations to the genotype. [ABSTRACT FROM AUTHOR]