Search results for "molecular epidemiology"
showing 10 items of 142 documents
HCV genotypes in Sicily: is there any evidence of a shift?
2009
The distribution of HCV strains in any area is characterized by a relative prevalence of one genotype, and a number of less prevalent types. In some Western countries a change from the prevalent HCV genotype 1 to genotypes 3 and 4 has been reported in the last decade. In order to assess possible variations of the distribution of HCV genotypes in Sicily, a southern region of Italy, a hospital-based cohort, collected prospectively, of 3,209 subjects with chronic HCV infection was surveyed, comparing the distribution of HCV genotypes during two consecutive periods, from 1997 to 2002 and from 2003 to 2007, according to age and gender. The results show that genotype 1b, which has been historical…
Molecular epidemiology of tuberculosis in Sicily, Italy: what has changed after a decade?
2014
Background We aimed to investigate the molecular epidemiology of Mycobacterium tuberculosis complex (MTBC) isolates in the province of Palermo, Sicily, Italy, by characterizing 183 isolates identified in the years 2004-2012. A comparison with 104 MTBC strains identified in the same geographic area in the years 1994-2000 was also carried out. Methods One hundred eighty-three MTBC isolates identified in Palermo, Italy, in the years 2004-2012 were analyzed by spoligotyping and the 24 mycobacterial interspersed repetitive unit (MIRU)-variable-number tandem-repeat (VNTR) method typing. Susceptibility testing to streptomycin, isoniazid, rifampin and ethambutol was also performed. Furthermore, the…
Variable geographic distribution of Blastocystis subtypes and its potential implications.
2012
Blastocystis is a common intestinal micro-eukaryote found in both humans and non-human hosts and known to be genetically very diverse. It has been divided into numerous subtypes (STs), nine of which have been identified in humans to date. Surveys of ST prevalence have started to emerge over the past few years but to date no data are available for any African country except Egypt and Tanzania. In this study, we determined the prevalence of Blastocystis STs in populations from Libya, Liberia and Nigeria, as well as expanding the dataset available for the UK. A total of 356 Blastocystis STs were identified in this study, 271 from the UK, 38 from Libya, 25 from Liberia and 22 from Nigeria. SSU …
Transmission of Drug-Resistant HIV Type 1 Strains in HAART-Naive Patients: A 5-Year Retrospective Study in Sicily, Italy
2010
The transmission of drug-resistant HIV-1 strains might compromise the efficacy of current first-line antiretroviral (ARV) regimens. Between 2004 and 2008, HIV-1 reverse transcriptase (RT) and protease (PR) genes of 108 ARVnaive Sicilian patients were amplified and sequenced to describe the prevalence of ARV resistance mutations among HAART-naive HIV-1-infected individuals. The frequency of transmitted drug resistance mutations (DRAMs) was determined by using genotypic interpretation algorithms. The proportion of HAART-naive HIV- 1-infected patients in Sicily increased from 18.4% to 23.5% during 2004–2008. Among naive patients, the overall prevalence of DRAMs was 15.7% [17/108; 95% CI: 9.4–2…
Epidemiological, clinical and molecular characterization of Lynch‐like syndrome: A population‐based study
2019
Colorectal carcinomas that are mismatch repair (MMR)‐deficient in the absence of MLH1 promoter methylation or germline mutations represent Lynch‐like syndrome (LLS). Double somatic events inactivating MMR genes are involved in the etiology of LLS tumors. Our purpose was to define the clinical and broader molecular hallmarks of LLS tumors and the population incidence of LLS, which remain poorly characterized. We investigated 762 consecutive colorectal carcinomas operated in Central Finland in 2000–2010. LLS cases were identified by a stepwise protocol based on MMR protein expression, MLH1 methylation and MMR gene mutation status. LLS tumors were profiled for CpG Island Methylator Phenotype (…
Molecular evolution and complete genome sequences in forensic analysis: Neisseria gonorrhoeae in a transmission case
2019
Molecular epidemiology and phylogenetic analyses are frequently used in the investigation of viral transmission cases in forensic contexts. Here, we present the methods and results of the analysis of a bacterial transmission in an alleged child abuse case using complete genome sequences obtained by high-throughput sequencing (HTS) methods.
Genotyping of Legionella pneumophila serogroup 1 strains isolated in Northern Sicily, Italy.
2008
During a three-year period, from April 2002 to May 2005, one hundred-forty-seven samples, taken from technical systems of water distribution at point of use, were repeatedly collected at six different sites in Northern Sicily and assayed for the presence of Legionella pneumophila serogroup 1 and serogroups 2 to 14. At the first samplings, the water distribution systems of all the sites were heavily contaminated, and disinfection treatments by the superheat and flush method were therefore performed. Treatments were always successful against L. pneumophila sg.1, but only in a few cases against all other serogroups. Eighty-six strains of L. pneumophila sg. 1, isolated from 26 of these samples,…
Fast and low-cost decentralized surveillance of transmission of tuberculosis based on strain-specific PCRs tailored from whole genome sequencing data…
2015
Molecular epidemiology has transformed our knowledge of how tuberculosis (TB) is transmitted. Whole genome sequencing (WGS) has reached unprecedented levels of accuracy. However, it has increased technical requirements and costs, and analysis of data delays results. Our objective was to find a way to reconcile speed and ease of implementation with the high resolution of WGS. The targeted regional allele-specific oligonucleotide PCR (TRAP) assay presented here is based on allele-specific PCR targeting strain-specific single nucleotide polymorphisms, identified from WGS, and makes it possible to track actively transmitted Mycobacterium tuberculosis strains. A TRAP assay was optimized to track…
Molecular relationship among Salmonella dublin isolates identified at the Center for Enterobacteriaceae of Palermo during the years 1971-85.
1987
SUMMARYA molecular epidemiological study was carried out on 60Salmonella dublinisolates identified at the Southern Italy Enterobacteriaceae Center between 1971 and 1985. These included 23 isolates from children with diarrhoea in Palermo obtained during 1984.All isolates from the outbreak of gastroenteritis in children were resistant to chloramphenicol and streptomycin and harboured two plasmids of 50 MDa and 3 MDa molecular weight, whereas the majority of the isolates identified before 1984 were susceptible to these antibiotics and carried only a 50 MDa molecular weight plasmid. FourS. dublinstrains successively identified from cattle (Palermo, Foggia, Portici) and from a child (Palermo) we…
Whole genome sequencing analysis of intrapatient microevolution in Mycobacterium tuberculosis: potential impact on the inference of tuberculosis tran…
2013
Background. It has been accepted that the infection by Mycobacterium tuberculosis (M. tuberculosis) can be more heterogeneous than considered. The emergence of clonal variants caused by microevolution events leading to population heterogeneity is a phenomenon largely unexplored. Until now, we could only superficially analyze this phenomenon by standard fingerprinting (RFLP and VNTR).Methods. In this study we applied whole genome sequencing for a more in-depth analysis of the scale of microevolution both at the intrapatient and interpatient scenarios.Results. We found that the amount of variation accumulated within a patient can be as high as that observed between patients along a chain of t…