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Search Results: 1 - 10 of 410089 matches for " Frank M?ller Aarestrup "
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In Silico Prediction of Human Pathogenicity in the γ-Proteobacteria
Massimo Andreatta,Morten Nielsen,Frank Mller Aarestrup,Ole Lund
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0013680
Abstract: Although the majority of bacteria are innocuous or even beneficial for their host, others are highly infectious pathogens that can cause widespread and deadly diseases. When investigating the relationships between bacteria and other living organisms, it is therefore essential to be able to separate pathogenic organisms from non-pathogenic ones. Using traditional experimental methods for this purpose can be very costly and time-consuming, and also uncertain since animal models are not always good predictors for pathogenicity in humans. Bioinformatics-based methods are therefore strongly needed to mine the fast growing number of genome sequences and assess in a rapid and reliable way the pathogenicity of novel bacteria.
PathogenFinder - Distinguishing Friend from Foe Using Bacterial Whole Genome Sequence Data
Salvatore Cosentino, Mette Voldby Larsen, Frank Mller Aarestrup, Ole Lund
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0077302
Abstract: Although the majority of bacteria are harmless or even beneficial to their host, others are highly virulent and can cause serious diseases, and even death. Due to the constantly decreasing cost of high-throughput sequencing there are now many completely sequenced genomes available from both human pathogenic and innocuous strains. The data can be used to identify gene families that correlate with pathogenicity and to develop tools to predict the pathogenicity of newly sequenced strains, investigations that previously were mainly done by means of more expensive and time consuming experimental approaches. We describe PathogenFinder (http://cge.cbs.dtu.dk/services/PathogenF?inder/), a web-server for the prediction of bacterial pathogenicity by analysing the input proteome, genome, or raw reads provided by the user. The method relies on groups of proteins, created without regard to their annotated function or known involvement in pathogenicity. The method has been built to work with all taxonomic groups of bacteria and using the entire training-set, achieved an accuracy of 88.6% on an independent test-set, by correctly classifying 398 out of 449 completely sequenced bacteria. The approach here proposed is not biased on sets of genes known to be associated with pathogenicity, thus the approach could aid the discovery of novel pathogenicity factors. Furthermore the pathogenicity prediction web-server could be used to isolate the potential pathogenic features of both known and unknown strains.
Regulation of the erm(C) Gene in Staphylococci from Reservoir with Different Usage of Macrolides
Lars B Jensen, Frank M Aarestrup
Acta Veterinaria Scandinavica , 2005, DOI: 10.1186/1751-0147-46-163
Abstract: Large amounts of the macrolide tylosin have been used for pig production in Denmark for growth promotion and therapy [1]. In 1996 68,350 kg of tylosin was used for growth promotion and 1,350 kg for therapy. No macrolides have been used for growth promotion for cattle but spiramycin and tylosin have been used therapeutically for treatment of mastitis [3]. A total of 644 kg macrolides, primarily tylosin, was used for cattle in 1996 in Denmark. Local variations in treatment strategies exist depending on the choice of the veterinarian but due to the used strain collection this effect will be minimal. At the same time 5,934 kg of penicillin was used (Erik Jacobsen, personal communication). The usage of macrolides for treatment of infections in human in general practice constitutes approximately 20–25 percent of the total usage of antibiotics in humans. However, in human medicine 16-membered macrolides are not used. The macrolides used in human medicine in Denmark are primarily erythromycin (14-membered) and azithromycin [2].A total of 185 macrolide resistant staphylococci were tested, twenty-nine staphylococci from cattle (8 Staphylococcus aureus and 21 coagulase negative staphylococci (CNS)), 111 Staphylococcus hyicus isolates of porcine origin and 45 S. aureus from non-hospitalized humans [4]. All animal isolates were obtained from the DANMAP surveillance program with one isolate per herd hereby representing a broad spectrum of farms in Denmark. Human isolates were obtained from individuals of both sex and from different age groups. All human, bovine and 96 porcine isolates were collected from 1995 to 1998. The remaining 15 porcine isolates were collected in 2001, two years after the discontinued usage of growth promoters in Denmark.The presence of erm(C) was confirmed using previous described primers [4]. Among the animal isolates from 1995–98, all except one porcine isolate contained the erm(C) gene (Table 1). erm(C) was found in 23 (69%) of the human isolates and 7
猪链球菌2型可能的毒力基因分布
田云,frank,m.,aarestrup,陆承平**
农业生物技术学报 , 2004,
Abstract:
Found of Putative Virulent Genes of Streptotoccus suis Type 2 Strains
猪链球菌2型可能的毒力基因的发现

TIAN Yun~,
田云
,Frank,M,Aarestrup,陆承平

微生物学报 , 2004,
Abstract: 猪链球菌2型(SS2)感染已成为影响全世界养猪业的重要问题之一。SS2菌株可分为毒力株、弱毒力株和无毒力株,但目前尚无区分此3类菌株的快速、有效的检测方法。为了获得毒力株特异的基因序列,对毒力株HA9801及无毒力株12^#进行了抑制性差减杂交(SSH)实验,获得了5个可能的新的毒力基因片段,分别是转录调节子、氨基酸通透酶、ABC转运子及表面锚定蛋白,在国内外尚属首次报道。这一发现将有助于区分SS2型菌株的毒力类型,并为SS2毒力株检测方法的建立奠定基础。
SCCmec Type IX Element in Methicillin Resistant Staphylococcusaureusspa Type t337 (CC9) Isolated from Pigs and Pork in Thailand
Pantip Sirichote,Frank M. Aarestrup,Rene S. Hendriksen
Frontiers in Microbiology , 2012, DOI: 10.3389/fmicb.2012.00103
Abstract: Methicillin resistant Staphylococcus aureus (MRSA) have emerged among livestock in several countries. In this study, we describe the results of a screening performed in pigs and raw pork samples in Thailand. Ten pork samples and 15 nasal swabs from pigs were collected from 2 markets and 1 pig farm in the Samuth Songkhram province in Thailand. MRSA were isolated using selective isolation procedures and confirmed by mecA PCR. The MRSA were characterized by antimicrobial susceptibility testing, pulsed field gel electrophoresis (PFGE), spa typing, SCCmec typing, and MLST. Resistance and virulence markers were screened using a microarray. Five of the pork samples and six pig nasal swabs were positive for MRSA. All 11 isolates belonged to spa type t337 but showed diversity in antimicrobial resistance patterns and PFGE profiles. Additionally, the isolates were sequence-typed; ST9, ST2136, ST2278 belonging to the clonal complex; CC9. All isolates harbored SCCmec IX and were resistant to 7 out of 14 tested antimicrobials; additional resistances to all antimicrobials tested were found in some of the pork and pig isolates and 1 pork isolate was resistant to 13 antimicrobials tested. Microarray analysis identified blaZ, aac-aphD, vga(A), tetM, and a tet efflux marker, in all strains and additionally ermB and aadD, cat and fex(A) in the pork isolates. None of the isolates were found PVL-positive, but enterotoxins were identified in all isolates. To our knowledge, only a few descriptions of MRSA in livestock and food products in Thailand have been observed but this is the first observation of MRSA CC9 associated with SCCmec IX in pork. This study indicates a likely widespread distribution of MRSA in pig and pork in Thailand and further investigation on the prevalence and importance of livestock associated MRSA in Thailand is needed.
The Discounting Confusion: An Ecological Economics Perspective Confusión en la tasa de descuento: una perspectiva desde la economía ecológica
Frank G. Müller
Revista Economía , 2013,
Abstract: Factors impacting on the discounting process are mirrored in every aspect of human activities, be it the philosophical, the aesthetic, the religious through to the environmental and scientific experiences. In short, discounting is a controversial concept, and yet, the economic profession seems to ignore that issues related to “long-term” discounting are complex, multifaceted, and far from settled. The environmental community in particular has expressed reservations about discounting, because this process —an inherently myopic one— embodies a built-in bias against the future generations.It will be argued here that the danger to ecological sustainability is of a specific nature, namely,it relates to the lack of substitutability between human-made capital and natural capital. If this assumption is accepted, then it follows that using a discount rate is an inadequate instrumentfor achieving sustainability. Thus, it will be argued that the implementation of the precautionary principle, e.g., in form of “safe minimum standards” of ecosystem protection, provides a successful approach for achieving sustainability. Los factores que influyen en el proceso de descuento se reflejan en todos los aspectos de la actividad humana, ya sea lo filosófico, lo estético o lo religioso a través de las experiencias ambientales y científicas. En resumen, el descuento es un concepto controvertido, y, sin embargo, la profesión económica parece ignorar que las cuestiones relacionadas al descuento de “largo plazo” son complejas, multifacéticas, y lejos de resolverse. La comunidad ambientalista, en particular, haexpresado reservas acerca del descuento, ya que este proceso —uno inherentemente miope—incorpora un sesgo implícito contra las futuras generaciones. Se argumenta que el peligro para la sostenibilidad ecológica es de carácter específico, es decir, que se refiere a la falta de posibilidad de sustitución entre el capital hecho por el hombre y el capital natural. Si se acepta esta hipótesis, entonces se deduce que el uso de una tasa de descuento es un instrumento inadecuado para el logro de la sostenibilidad. Por lo tanto, se puede argumentar que la aplicación del principio de precaución, por ejemplo, en la forma de “normas mínimas de seguridad” de protección del ecosistema, proporciona un enfoque exitoso para lograr la sostenibilidad.
Transnacionalización e informalidad en las políticas de rescate en el centro histórico de Ciudad de México
Frank Müller
Boletín Científico Sapiens Research , 2011,
Abstract: This article focuses on the role of informality in the construction of the Historic Centre of Mexico City. It argues that the applied rescue poli-tics, sustaining this construction, have a transnational dimension that can be seen, first, in the commodification, that is, the capitalization of archi-tecture by private and public investment, second, in the definition as cultural heritage of humanity by the UNESCO in 1987 and third, in local politics of spatial ordering, that, legitimated by a security discourse, relies on the expertise of ex-mayor of New York, Rudolf Giuliani. This multidimensional process involves further socio-spatial exclusion from the central area.
Resistance to penicillin of Staphylococcus aureus isolates from cows with high somatic cell counts in organic and conventional dairy herds in Denmark
Torben W Bennedsgaard, Stig M Thamsborg, Frank M Aarestrup, Carsten Enevoldsen, Mette Vaarst, Anna B Christoffersen
Acta Veterinaria Scandinavica , 2006, DOI: 10.1186/1751-0147-48-24
Abstract: 20 conventional herds, 18 organic herds that converted before 1995, and 19 herds converting to organic farming in 1999 or 2000 were included in the study. Herds converting to organic farming were sampled three times one year apart; the other herds were sampled once. Risk of infection was estimated based on somatic cell count, milk production, breed, age and lactation stage.The high-risk cows represented about 49 % of the cows in the herds. The overall prevalence of SA and SAr among these cows was 29% (95% confidence interval: 24%–34%) and 4% (95% confidence interval: 2%–5%) respectively. The prevalence of penicillin resistance among SA infected cows was 12% (95% confidence interval: 6%–19%) when calculated from the first herd visits. No statistically significant differences were observed in the prevalence of SAr or the proportion of isolates resistant to penicillin between herd groups.The proportion of isolates resistant to penicillin was low compared to studies in other countries except Norway and Sweden. Based on the low prevalence of penicillin resistance of SA, penicillin should still be the first choice of antimicrobial agent for treatment of bovine intramammary infection in Denmark.Staphylococcus aureus (SA) is the most commonly occurring pathogen in udder quarters with elevated somatic cell counts (SCC) in Denmark and accounts for approximately 50% of the intramammary infections of lactating cows [1]. Experimental infections with SA have shown that infected cows develop high SCC, though both the SCC and the number of bacteria shed in the milk vary considerably both between cows and within quarters over time [2]. The control of SA infections in dairy herds often includes a combination of preventive measures to reduce the number of new infections, dry cow treatment of all cows with antibiotics, treatment of infected animals, and culling of chronically infected animals [3,4]. Frequent use of antibiotic treatment in dairy cows has been proposed to comprise a risk
Evaluation of Whole Genome Sequencing for Outbreak Detection of Salmonella enterica
Pimlapas Leekitcharoenphon, Eva M. Nielsen, Rolf S. Kaas, Ole Lund, Frank M. Aarestrup
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0087991
Abstract: Salmonella enterica is a common cause of minor and large food borne outbreaks. To achieve successful and nearly ‘real-time’ monitoring and identification of outbreaks, reliable sub-typing is essential. Whole genome sequencing (WGS) shows great promises for using as a routine epidemiological typing tool. Here we evaluate WGS for typing of S. Typhimurium including different approaches for analyzing and comparing the data. A collection of 34 S. Typhimurium isolates was sequenced. This consisted of 18 isolates from six outbreaks and 16 epidemiologically unrelated background strains. In addition, 8 S. Enteritidis and 5 S. Derby were also sequenced and used for comparison. A number of different bioinformatics approaches were applied on the data; including pan-genome tree, k-mer tree, nucleotide difference tree and SNP tree. The outcome of each approach was evaluated in relation to the association of the isolates to specific outbreaks. The pan-genome tree clustered 65% of the S. Typhimurium isolates according to the pre-defined epidemiology, the k-mer tree 88%, the nucleotide difference tree 100% and the SNP tree 100% of the strains within S. Typhimurium. The resulting outcome of the four phylogenetic analyses were also compared to PFGE reveling that WGS typing achieved the greater performance than the traditional method. In conclusion, for S. Typhimurium, SNP analysis and nucleotide difference approach of WGS data seem to be the superior methods for epidemiological typing compared to other phylogenetic analytic approaches that may be used on WGS. These approaches were also superior to the more classical typing method, PFGE. Our study also indicates that WGS alone is insufficient to determine whether strains are related or un-related to outbreaks. This still requires the combination of epidemiological data and whole genome sequencing results.
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