Search results for "Sequence analysis"
showing 10 items of 1349 documents
GyrA sequence-based typing of Legionella.
2000
Comparative sequence analysis of a 423-bp segment of the gyrA gene including a region homologous to the quinolone resistance-determining region (QRDR) of other species was evaluated as a novel typing method for Legionella strains. The study was performed with 29 reference strains representing 11 different Legionella species, with various serogroups, and with 13 clinical isolates of L. pneumophila. Pulsed-field gel electrophoresis and serotyping were employed for comparison of the clinical isolates. QRDR sequencing proved to be a highly discriminative tool for typing Legionellae, and permitted identification of species, serogroups and even different strains within serogroup 1. None of the is…
Norovirus GII.4/Sydney/2012 in Italy, Winter 2012–2013
2013
To the Editor: Noroviruses (NoVs) are the major cause of acute gastroenteritis in children and adults; they are responsible for sporadic cases and outbreaks of gastroenteritis in various epidemiologic settings. NoVs can be classified genetically into at least 5 genogroups, GI to GV (1). Although >30 genotypes within genogroups GI, GII, and GIV can infect humans (2), a single genotype, GII.4, has been associated with most NoV-related outbreaks and sporadic cases of gastroenteritis worldwide (3). GII.4 NoV strains continuously undergo genetic/antigenic diversification and periodically generate novel strains through accumulation of punctate mutations or recombination. New GII.4 variants emerge…
Lineage diversification and recombination in type-4 human astroviruses.
2013
Abstract Human astroviruses (HAstVs) are important enteric pathogens and can be classified genetically and antigenically into eight types. During surveillance of HAstVs in Italy, type-4 HAstVs were detected only sporadically and found to cluster into two distinct genetic groups. Upon sequence analysis of the 3′ end of the polymerase gene (ORF1b) and of the full-length ORF2, the 2008 type-4 HAstV strains were characterised as a novel ORF2 genetic lineage, designated as 4c. The 2008 type-4 HAstVs also shared the ORF1b gene with similar HAstV-4c strains detected globally, thus displaying a conserved ORF1b/ORF2 asset. By interrogation of the databases, this novel lineage 4c accounted for 60.8% …
Evidence for recombination between the pandemic GII.4 norovirus strains New Orleans 2009 and Sydney 2012
2013
ABSTRACT During 2012, a novel pandemic GII.4 norovirus variant, Sydney 2012, emerged worldwide. A signature of the variant was a GII.Pe ORF1, in association with GII.4 Apeldoorn 2008-like ORF2-ORF3 genes. We report the detection of recombinant GII.4 Sydney 2012 strains, possessing the ORF1 gene of the former pandemic variant New Orleans 2009.
Surveillance of human astrovirus circulation in Italy 2002-2005: emergence of lineage 2c strains.
2010
AbstractBy screening faecal samples collected over four consecutive years (2002-2005) from hospitalized children with diarrhoea in Palermo, Italy, astroviruses (HAstVs) were detected in 3.95% of the patients. The predominant type circulating was HAstV-1 but, in 2002, only HAstV-2 and -4 were identified. Interestingly, the HAstVs-2 detected appeared to be consistently different in 5′ end of their open reading frame 2 from the previously described subtypes. These novel type 2 strains were included in a new 2c lineage based on the phylogenetic analysis and the presence of nine peculiar substitutions.
Recombinant norovirus GII.g/GII.12 gastroenteritis in children.
2011
Recombinant GII.g/GII.12 norovirus (NoV) strains emerged in 2008 in Australia and subsequently have been associated with gastroenteritis outbreaks worldwide. In the winter season 2009-2010 GII.12 strains caused 16% of the NoV outbreaks in the United States. During 2009-2010 we also identified GII.g/GII.12 strains during surveillance of sporadic cases of gastroenteritis in Italian children. Severity scores were calculated for the GII.g/GII.12 NoV infections using the Vesikari scale and in two out of three paediatric cases they exceeded the median value calculated for concomitant GII.4 infections. Upon sequence analysis, the Italian strains were found to be recombinant viruses and displayed d…
Genetic heterogeneity and recombination in human type 2 astroviruses
2012
ABSTRACT Novel lineages of human astrovirus (HAstV) types 2, 2c, and 2d have been identified. Upon sequencing of the 3′ end of the genome, the type 2c and 2d HAstVs were found to be open reading frame 1b (ORF1b)-ORF2 recombinant, with ORF1b being derived from type 3 and type 1 HAstVs, respectively. An ORF2 interlineage recombinant strain, 2c/2b, was also identified.
Simultaneous identification of campylobacters and prediction of quinolone resistance by comparative sequence analysis.
1997
Comparative sequence analysis of a 30-bp segment in the quinolone resistance-determining region of campylobacters not only allows for the detection of base changes associated with resistance but also is a powerful tool for species identification based on silent mutations.
Metagenomics of human microbiome: beyond 16s rDNA.
2012
Clin Microbiol Infect 2012; 18 (Suppl. 4): 4749 Abstract The gut microbiota presents a symbiotic relationship with the human host playing a beneficial role in human health. Since its establishment, the bacterial community is subjected to the influence of many different factors that shape its composition within each individual. However, an important convergence is observed at functional level in the gut microbiota. A metatranscriptomic study of healthy individuals showed homogeneity in the composition of the active microbiota that increased further at functional level.
Molecular Epidemiology of Caliciviruses Causing Outbreaks and Sporadic Cases of Acute Gastroenteritis in Spain
2002
ABSTRACT The molecular epidemiology of human caliciviruses (HuCVs) causing sporadic cases and outbreaks of acute gastroenteritis around eastern Spain (Catalonia and the Valencian Community) was studied by reverse transcription-PCR (RT-PCR) and by sequencing part of the RNA polymerase gene in open reading frame 1. HuCVs were detected in 44 of 310 stool specimens (14.19%) negative for other enteric pathogens obtained from children with acute gastroenteritis. Norwalk-like viruses (NLVs) were the most common cause of the gastroenteritis outbreaks investigated here. They were detected in 14 out of 25 (56%) outbreaks with an identified pathogen. Genotypes producing both sporadic cases and outbrea…