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Article
Open AccessCorrecting modification-mediated errors in nanopore sequencing by nucleotide demodification and reference-based correction
The accuracy of Oxford Nanopore Technology (ONT) sequencing has significantly improved thanks to new flowcells, sequencing kits, and basecalling algorithms. However, novel modification types untrained in the b...
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Article
Open AccessPGAdb-builder: A web service tool for creating pan-genome allele database for molecular fine ty**
With the advance of next generation sequencing techniques, whole genome sequencing (WGS) is expected to become the optimal method for molecular subty** of bacterial isolates. To use WGS as a general subtypin...
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Article
Erratum: Global phylogeography and evolutionary history of Shigella dysenteriae type 1
Nature Microbiology 1, 16027 (2016); published 21 March 2016; corrected 3 October 2016 In the original version of this Letter, co-author Simon Le Hello's name was coded wrongly resulting in it being incorrect ...
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Article
Global phylogeography and evolutionary history of Shigella dysenteriae type 1
Together with plague, smallpox and typhus, epidemics of dysentery have been a major scourge of human populations for centuries1. A previous genomic study concluded that Shigella dysenteriae type 1 (Sd1), the epid...
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Article
Open AccessInfrequent cross-transmission of Shigella flexneri 2a strains among villages of a mountainous township in Taiwan with endemic shigellosis
Shigellosis is rare in Taiwan, with an average annual incidence rate of 1.68 cases per 100,000 persons in 2000–2007. However, the incidence rate for a mountainous township in eastern Taiwan, Zhuoxi, is 60.2 ti...
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Article
Open AccessCombined rpo B duplex PCR and hsp65 PCR restriction fragment length polymorphism with capillary electrophoresis as an effective algorithm for identification of Mycobacterial species from clinical isolates
Mycobacteria can be quickly and simply identified by PCR restriction-enzyme analysis (PRA), but misidentification can occur because of similarities in band sizes that are critical for discriminating among spec...
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Article
Open AccessCharacterization of Shigella sonnei in Malaysia, an increasingly prevalent etiologic agent of local shigellosis cases
Shigellosis is a major public health concern worldwide, especially in develo** countries. It is an acute intestinal infection caused by bacteria of the genus Shigella, with a minimum infective dose as low as 10...
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Article
Open AccessAssessment of hypermucoviscosity as a virulence factor for experimental Klebsiella pneumoniaeinfections: comparative virulence analysis with hypermucoviscosity-negative strain
Klebsiella pneumoniae displaying the hypermucoviscosity (HV) phenotype are considered more virulent than HV-negative strains. Nevertheless, the emergence of tissue-abscesses-associated HV-negative isolates motiva...
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Article
Open AccessCharacterization of 13 multi-drug resistant Salmonella serovars from different broiler chickens associated with those of human isolates
Salmonella are frequently isolated from chickens and their products. Prevalent serogroups and serovars of Salmonella as well as their genotypes and antibiograms were determined for cloacal samples from 1595 chick...
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Article
Open AccessMultilocus variable-number tandem repeat analysis for molecular ty** and phylogenetic analysis of Shigella flexneri
Shigella flexneri is one of the causative agents of shigellosis, a major cause of childhood mortality in develo** countries. Multilocus variable-number tandem repeat (VNTR) analysis (MLVA) is a prominent subtyp...
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Article
Open AccessClonal dissemination of the multi-drug resistant Salmonella enterica serovar Braenderup, but not the serovar Bareilly, of prevalent serogroup C1 Salmonella from Taiwan
Nontyphoidal Salmonella is the main cause of human salmonellosis. In order to study the prevalent serogroups and serovars of clinical isolates in Taiwan, 8931 Salmonellae isolates were collected from 19 medical c...
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Article
Open AccessAssociation of the shuffling of Streptococcus pyogenes clones and the fluctuation of scarlet fever cases between 2000 and 2006 in central Taiwan
The number of scarlet fever occurrences reported between 2000 and 2006 fluctuated considerably in central Taiwan and throughout the nation. Isolates of Streptococcus pyogenes were collected from scarlet fever pat...
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Article
Open AccessUse of a multilocus variable-number tandem repeat analysis method for molecular subty** and phylogenetic analysis of Neisseria meningitidis isolates
The multilocus variable-number tandem repeat (VNTR) analysis (MLVA) technique has been developed for fine ty** of many bacterial species. The genomic sequences of Neisseria meningitidis strains Z2491, MC58 and ...
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Article
Open AccessMolecular epidemiology and emergence of worldwide epidemic clones of Neisseria meningitidis in Taiwan
Meningococcal disease is infrequently found in Taiwan, a country with 23 million people. Between 1996 and 2002, 17 to 81 clinical cases of the disease were reported annually. Reported cases dramatically increa...
