Search results for "Molecular Epidemiology"
showing 10 items of 142 documents
Temporal variation in the distribution of type-1 human astrovirus lineages in a settled population over 14 years.
2016
Human astroviruses (HAstVs) are important enteric pathogens that are genetically and antigenically heterogeneous and can be classified into eight sero/genotypes (HAstV-1 to -8) and different lineages within each HAstV type. This study describes the genetic diversity of HAstVs circulating in southern Italy over 14 years. Molecular analysis of HAstV-1 strains showed that three different lineages (1a, 1b and 1d) of the predominant genotype were circulating during the study period. The study of an archival collection of HAstV strains offers a unique opportunity to evaluate the patterns of variation of HAstV infections over the years and to correlate the observed epidemiological changes to the g…
Diversity, virulence, and antimicrobial resistance of the KPC-producing Klebsiella pneumoniae ST307 clone
2017
ABSTRACT : The global spread of Klebsiella pneumoniae producing Klebsiella pneumoniae carbapenemase (KPC) has been mainly associated with the dissemination of high-risk clones. In the last decade, hospital outbreaks involving KPC-producing K. pneumoniae have been predominantly attributed to isolates belonging to clonal group (CG) 258. However, results of recent epidemiological analysis indicate that KPC-producing sequence type (ST) 307, is emerging in different parts of the world and is a candidate to become a prevalent high-risk clone in the near future. Here we show that the ST307 genome encodes genetic features that may provide an advantage in adaptation to the hospital environment and t…
Whole genome sequencing-based analysis of tuberculosis (TB) in migrants: rapid tools for cross-border surveillance and to distinguish between recent …
2019
14 páginas, 7 figuras
Molecular evolution methods to study HIV-1 epidemics
2018
Nucleotide sequences of HIV isolates are obtained routinely to evaluate the presence of resistance mutations to antiretroviral drugs. But, beyond their clinical use, these and other viral sequences include a wealth of information that can be used to better understand and characterize the epidemiology of HIV in relevant populations. In this review, we provide a brief overview of the main methods used to analyze HIV sequences, the data bases where reference sequences can be obtained, and some caveats about the possible applications for public health of these analyses, along with some considerations about their limitations and correct usage to derive robust and reliable conclusions.
Molecular epidemiology of Acinetobacter baumannii in Iran: endemic and epidemic spread of multiresistant isolates
2014
Objectives We examined the molecular epidemiology of Acinetobacter baumannii clinical isolates from two cities (Tehran and Tabriz) of Iran. Methods DiversiLab repetitive extragenic palindromic PCR (rep-PCR), multilocus sequence typing and sequence group multiplex PCR were performed. The presence of resistance mechanisms including metallo-β-lactamases, extended-spectrum β-lactamases, OXA carbapenemases, aminoglycoside-modifying enzymes and RNA methylases was also investigated. Results DiversiLab rep-PCR identified 11 clusters and 11 singleton isolates. Twelve sequence types (STs), including six novel types, were identified. Sequence groups (SGs) 1-3 as well as five additional banding pattern…
Dissemination of a Carbapenem-Resistant Acinetobacter baumannii Strain Belonging to International Clone II/Sequence Type 2 and Harboring a Novel AbaR…
2013
ABSTRACT An outbreak of hospital-acquired Acinetobacter baumannii infections, caused by a bla OXA-23 -positive carbapenem-resistant strain belonging to international clone II/ST2, was detected in Latvia. The strain was partially equipped with the armA gene and the intI1-aacA4-catB8-aadA1-qacE Δ 1 class 1 integron. In addition, the strain carried AbaR25, a novel AbaR4-like resistance island of ∼46,500 bp containing structures similar to the previously described AbaR22 and Tn 6167 islands. AbaR25 was characterized by the occurrence of a second copy of Tn 6022a interrupted by Tn 2006 carrying the bla OXA-23 gene.
Occult Hepatitis B Infection in the Immigrant Population of Sicily, Italy.
2012
In Italy, about 7 % of the resident population is represented by immigrants originating from geographic regions at high endemicity for hepatitis B virus infection. This study aims to assess the prevalence of occult HBV infection (OBI) including the identification of HBV-genotypes in a population of immigrants serologically negative for hepatitis B surface antigen (HBsAg). Between May 2006 and May 2010, 339 immigrants were tested for markers of HBV, hepatitis C virus (HCV) and human immunodeficiency virus (HIV) infections. HBV-DNA was tested by using nested-PCR assays on three different genetic region. HBV-DNA was detected in plasma samples of 11/339 (3.2 %) patients. Most of them had no ser…
Dynamics and molecular evolution of HIV-1 strains in Sicily among antiretroviral naïve patients.
2012
Abstract HIV-1 subtype B is the most frequent strain in Sicily. To date, there is no available data about the genetic diversity of HIV-1 viral strains circulating in Sicily among antiretroviral (ARV) naive subjects and the role of immigration as potential determinant of evolutionary dynamics of HIV-1 molecular epidemiology. For this purpose, HIV-1 polymerase (pol) sequences obtained from 155 ARV naive individuals from 2004 to 2009 were phylogenetically analysed. The overall rate of HIV-1 non-B infections was 31.0% (n = 48/155), increasing from 7.8% in 2004–2006 to 40.9% in 2009, and about one-third were identified as unique recombinant forms. CRF02_AG was the prevalent non-B clade (n = 28/4…
Rotavirus genotypes co-circulating in Europe between 2006 and 2009 as determined by EuroRotaNet, a pan-European collaborative strain surveillance net…
2011
SUMMARYEuroRotaNet, a laboratory network, was established in order to determine the diversity of co-circulating rotavirus strains in Europe over three or more rotavirus seasons from 2006/2007 and currently includes 16 countries. This report highlights the tremendous diversity of rotavirus strains co-circulating in the European population during three years of surveillance since 2006/2007 and points to the possible origins of these strains including genetic reassortment and interspecies transmission. Furthermore, the ability of the network to identify strains circulating with an incidence of ⩾1% allowed the identification of possible emerging strains such as G8 and G12 since the beginning of…
Genetic Diversity of HIV-1 Non-B Strains in Sicily: Evidence of Intersubtype Recombinants by Sequence Analysis ofgag,pol, andenvGenes
2007
The molecular epidemiology of HIV-1 strains in Sicily (Italy) was phylogenetically investigated by the analysis of HIV-1 gag, pol, and env gene sequences from 11 HIV-1 non-B strains from 408 HIV-1-seropositive patients observed from September 2001 to August 2006. Sequences suggestive of recombination were further investigated by bootscanning analysis of various fragments. Overall, we identified several second-generation recombinant (SGRs) strains, which contained genetic material of CRF02_AG in at least one gene. Notably, three individuals were found to be infected with subsubtype A3, and one of them showed genetic recombination with subsubtype A4. The current study emphasizes the genetic a…