Bacterial infection in association with snakebite: A 10-year experience in a northern Taiwan medical center

BackgroundMicrobiological data of secondary wound infections following snakebites is rarely reported in Taiwan. The objective of this study was to assess the secondary wound infection after venomous snakebites.MethodsWe conducted a 10-year retrospective survey on patients admitted for venomous snakebites and microbiological data of wound cultures at a medical center in northern Taiwan.ResultsBetween April 2001 and April 2010, 231 patients who experienced snakebites were included. Male predominated, accounting for 62.3% (144). The age range of patients was 4–95 years. Ninety-five (41.1%) people were bitten by Trimeresurus mucrosquamatus, followed by Tstejnegeri, and cobra. A total of 61 pathogens were obtained from 21 patients. Thirty-nine (63.9%) isolates were gram-negative bacteria, 14 (23%) gram-positive pathogens, and 8 (13.1%) anaerobic pathogens. There were 17 patients bitten by cobra in these 21 patients. Morganella morganii and Enterococcus species were the most common pathogens identified in the wound cultures.ConclusionCobra bite causes more severe bacterial infection than other kinds of snakebites. Oral amoxicillin/clavulanate plus ciprofloxacin or parenteral piperacillin/tazobactam alone can be the choices for empirical or definitive treatment, and surgical intervention should be considered for established invasive soft tissue infections

Genomic diversity of citrate fermentation in Klebsiella pneumoniae

<p>Abstract</p> <p>Background</p> <p>It has long been recognized that <it>Klebsiella pneumoniae </it>can grow anaerobically on citrate. Genes responsible for citrate fermentation of <it>K. pneumoniae </it>were known to be located in a 13-kb gene cluster on the chromosome. By whole genome comparison of the available <it>K. pneumoniae </it>sequences (MGH 78578, 342, and NTUH-K2044), however, we discovered that the fermentation gene cluster was present in MGH 78578 and 342, but absent in NTUH-K2044. In the present study, the previously unknown genome diversity of citrate fermentation among <it>K. pneumoniae </it>clinical isolates was investigated.</p> <p>Results</p> <p>Using a genomic microarray containing probe sequences from multiple <it>K. pneumoniae </it>strains, we investigated genetic diversity among <it>K. pneumoniae </it>clinical isolates and found that a genomic region containing the citrate fermentation genes was not universally present in all strains. We confirmed by PCR analysis that the gene cluster was detectable in about half of the strains tested. To demonstrate the metabolic function of the genomic region, anaerobic growth of <it>K. pneumoniae </it>in artificial urine medium (AUM) was examined for ten strains with different clinical histories and genomic backgrounds, and the citrate fermentation potential was found correlated with the genomic region. PCR detection of the genomic region yielded high positive rates among a variety of clinical isolates collected from urine, blood, wound infection, and pneumonia. Conserved genetic organizations in the vicinity of the citrate fermentation gene clusters among <it>K. pneumoniae</it>, <it>Salmonella enterica</it>, and <it>Escherichia coli </it>suggest that the13-kb genomic region were not independently acquired.</p> <p>Conclusion</p> <p>Not all, but nearly half of the <it>K. pneumoniae </it>clinical isolates carry the genes responsible for anaerobic growth on citrate. Genomic variation of citrate fermentation genes in <it>K. pneumoniae </it>may contribute to metabolic diversity and adaptation to variable nutrient conditions in different environments.</p

Fosmid library end sequencing reveals a rarely known genome structure of marine shrimp Penaeus monodon

<p>Abstract</p> <p>Background</p> <p>The black tiger shrimp (<it>Penaeus monodon</it>) is one of the most important aquaculture species in the world, representing the crustacean lineage which possesses the greatest species diversity among marine invertebrates. Yet, we barely know anything about their genomic structure. To understand the organization and evolution of the <it>P. monodon </it>genome, a fosmid library consisting of 288,000 colonies and was constructed, equivalent to 5.3-fold coverage of the 2.17 Gb genome. Approximately 11.1 Mb of fosmid end sequences (FESs) from 20,926 non-redundant reads representing 0.45% of the <it>P. monodon </it>genome were obtained for repetitive and protein-coding sequence analyses.</p> <p>Results</p> <p>We found that microsatellite sequences were highly abundant in the <it>P. monodon </it>genome, comprising 8.3% of the total length. The density and the average length of microsatellites were evidently higher in comparison to those of other taxa. AT-rich microsatellite motifs, especially poly (AT) and poly (AAT), were the most abundant. High abundance of microsatellite sequences were also found in the transcribed regions. Furthermore, <it>via </it>self-BlastN analysis we identified 103 novel repetitive element families which were categorized into four groups, <it>i.e</it>., 33 WSSV-like repeats, 14 retrotransposons, 5 gene-like repeats, and 51 unannotated repeats. Overall, various types of repeats comprise 51.18% of the <it>P. monodon </it>genome in length. Approximately 7.4% of the FESs contained protein-coding sequences, and the Inhibitor of Apoptosis Protein (IAP) gene and the Innexin 3 gene homologues appear to be present in high abundance in the <it>P. monodon </it>genome.</p> <p>Conclusions</p> <p>The redundancy of various repeat types in the <it>P. monodon </it>genome illustrates its highly repetitive nature. In particular, long and dense microsatellite sequences as well as abundant WSSV-like sequences highlight the uniqueness of genome organization of penaeid shrimp from those of other taxa. These results provide substantial improvement to our current knowledge not only for shrimp but also for marine crustaceans of large genome size.</p

Complexity of the Mycoplasma fermentans M64 Genome and Metabolic Essentiality and Diversity among Mycoplasmas

Recently, the genomes of two Mycoplasma fermentans strains, namely M64 and JER, have been completely sequenced. Gross comparison indicated that the genome of M64 is significantly bigger than the other strain and the difference is mainly contributed by the repetitive sequences including seven families of simple and complex transposable elements ranging from 973 to 23,778 bps. Analysis of these repeats resulted in the identification of a new distinct family of Integrative Conjugal Elements of M. fermentans, designated as ICEF-III. Using the concept of “reaction connectivity”, the metabolic capabilities in M. fermentans manifested by the complete and partial connected biomodules were revealed. A comparison of the reported M. pulmonis, M. arthritidis, M. genitalium, B. subtilis, and E. coli essential genes and the genes predicted from the M64 genome indicated that more than 73% of the Mycoplasmas essential genes are preserved in M. fermentans. Further examination of the highly and partly connected reactions by a novel combinatorial phylogenetic tree, metabolic network, and essential gene analysis indicated that some of the pathways (e.g. purine and pyrimidine metabolisms) with partial connected reactions may be important for the conversions of intermediate metabolites. Taken together, in light of systems and network analyses, the diversity among the Mycoplasma species was manifested on the variations of their limited metabolic abilities during evolution

Sequencing and Comparative Genome Analysis of Two Pathogenic Streptococcus gallolyticus Subspecies: Genome Plasticity, Adaptation and Virulence

Streptococcus gallolyticus infections in humans are often associated with bacteremia, infective endocarditis and colon cancers. The disease manifestations are different depending on the subspecies of S. gallolyticus causing the infection. Here, we present the complete genomes of S. gallolyticus ATCC 43143 (biotype I) and S. pasteurianus ATCC 43144 (biotype II.2). The genomic differences between the two biotypes were characterized with comparative genomic analyses. The chromosome of ATCC 43143 and ATCC 43144 are 2,36 and 2,10 Mb in length and encode 2246 and 1869 CDS respectively. The organization and genomic contents of both genomes were most similar to the recently published S. gallolyticus UCN34, where 2073 (92%) and 1607 (86%) of the ATCC 43143 and ATCC 43144 CDS were conserved in UCN34 respectively. There are around 600 CDS conserved in all Streptococcus genomes, indicating the Streptococcus genus has a small core-genome (constitute around 30% of total CDS) and substantial evolutionary plasticity. We identified eight and five regions of genome plasticity in ATCC 43143 and ATCC 43144 respectively. Within these regions, several proteins were recognized to contribute to the fitness and virulence of each of the two subspecies. We have also predicted putative cell-surface associated proteins that could play a role in adherence to host tissues, leading to persistent infections causing sub-acute and chronic diseases in humans. This study showed evidence that the S. gallolyticus still possesses genes making it suitable in a rumen environment, whereas the ability for S. pasteurianus to live in rumen is reduced. The genome heterogeneity and genetic diversity among the two biotypes, especially membrane and lipoproteins, most likely contribute to the differences in the pathogenesis of the two S. gallolyticus biotypes and the type of disease an infected patient eventually develops

A Corpus-based Approach to Automatic Compound Extraction

An automatic compound retrieval method is proposed to extract compounds within a text message. It uses n-gram mutual information, relative frequency count and parts of speech as the features for compound extraction. The problem is modeled as a two-class classification problem based on the distributional characteristics of n-gram tokens in the compound and the non-compound clusters. The recall and precision using the proposed approach are 96.2% and 48.2% for bigram compounds and 96.6% and 39.6% for trigram compounds for a testing corpus of 49,314 words. A significant cutdown in processing time has been observed

A New Quantitative Quality Measure for Machine Translation Systems

In lilts paper, an objective qtumtitafive quality incasure is protxsed to evaluate tile performance of machiuc translation systems. The proposed methcu3 is to compare the raw translation output of an MT system with the final revised version lbr the customers, and theu compute the editing efforts mquir to convert the mw translalion to the final version. lu contrast to the other prolx&gt;sals, the evaluation process can be done quickly and automatically. lienee, it can provide a quick response on any system change. A systen tiesigner can thus quickly lind the advantages or faults of a particular performanceimproving strategy anti improve system performance dynamically. Application of such a measure to improve the systen performance on-line on a parameterized and feedback-controlled system will be demonstrated. Furtilermore, because the revised version is used directly as a reference, the peffollllauce nleaSUl-e caB reflect tile real quality gap between the system perfoonance and customer expectation. A system designer can thus concentra e on practically impostor topics ruther than on theoretically interesting issues

ABSTRACT Design of Lexical Database for Financial Domain

In this paper, we study the design of domain lexicons and address the problems of lexical knowledge representation and linking between different knowledge sources. A domain lexicon contains substantial domain specific vocabularies with associated phonological, morphological, syntactic and semantic/pragmatic information as well as links to general knowledge bases which are rich enough to support knowledge-intensive models for practical NLP systems. We take financial domain as an example to illustrate the representation structures for syntactic and semantic knowledge. In order to suit for both maximal reusability and deep analysis, our domain lexicon is designed with uniform knowledge representation and fine-grain feature encoding. We also address the issues of how to bridge the gaps between coarse-grain general lexicons and fine-grain domain lexicons. Keywords: Lexical database, Ontology, Finance domain lexico