scholarly journals Genomic Comparison of Salmonella Enteritidis Strains Isolated from Laying Hens and Humans in the Abruzzi Region during 2018

Pathogens ◽  
2020 ◽  
Vol 9 (5) ◽  
pp. 349
Author(s):  
Lisa Di Marcantonio ◽  
Anna Janowicz ◽  
Katiuscia Zilli ◽  
Romina Romantini ◽  
Stefano Bilei ◽  
...  
Keyword(s):  
Salmonella Enteritidis ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Nucleotide Polymorphisms ◽  
Salmonella Enterica Serovar Enteritidis ◽  
Single Linkage ◽  
Multiple Loci ◽  
Perform Cluster Analysis ◽  
Foodborne Infection ◽  
Core Genes

Salmonellosis is a major cause of bacterial foodborne infection. Since 2016, an increased number of cases of gastroenteritis caused by Salmonella enterica serovar Enteritidis linked to eggs produced in Poland has been reported in Europe. In Italy, S. Enteritidis is one of the three most commonly reported serotypes, associated mainly with the consumption of contaminated eggs and derived products. In our work, we analysed 61 strains of S. Enteritidis obtained from humans and farms in the Abruzzi region, Italy, in 2018. We used Multiple-Loci Variable-Number Tandem Repeat (VNTR) analysis (MLVA)-based typing and Whole-Genome Sequencing (WGS) tools to identify closely related strains and perform cluster analysis. We found two clusters of genetically similar strains. The first one was present in the local farms and isolated from human cases and had single-linkage distance of no more than two core genes and less than five Single-Nucleotide Polymorphisms (SNPs). The second cluster contained strains isolated from humans and from a dessert (tiramisù) sample that shared identical core genome and were assigned the same SNP address. Cluster 2 isolates were found to be genetically similar to an S. Enteritidis strain from a multi-country outbreak linked to Polish eggs.

scholarly journals First Description of Macrolide-Resistant Mycoplasma pneumoniae in Adults with Community-Acquired Pneumonia in Italy

2019 ◽  
Vol 2019 ◽  
pp. 1-5 ◽  
Author(s):  
Daniela Loconsole ◽  
Anna Lisa De Robertis ◽  
Rosanna Mallamaci ◽  
Anna Sallustio ◽  
Anna Morea ◽  
...  
Keyword(s):  
Mycoplasma Pneumoniae ◽  
Variable Number Tandem Repeat ◽  
Point Mutations ◽  
Cross Sectional Study ◽  
Variable Number ◽  
Community Acquired Pneumonia ◽  
23S Rrna ◽  
Cross Sectional ◽  
South Italy ◽  
Multiple Loci

Background. Mycoplasma pneumoniae is a common cause of community-acquired pneumonia (CAP). This cross-sectional study aimed to determine the prevalence of macrolide-resistant M. pneumoniae strains in a convenience series of 234 adult hospitalised and nonhospitalised subjects with a diagnosis of CAP in January 2013 to April 2015 in South Italy. Methods. Respiratory samples were subjected to real-time PCR. In M. pneumoniae-positive samples, domain V of 23S rRNA was sequenced to detect resistance-conferring point mutations. P1 major adhesion protein typing and multiple loci variable-number tandem repeat analysis (MLVA) were also performed. Results. Of the 234 samples, 15 (6.4%) were positive for M. pneumoniae. Three of these had a macrolide-resistant genotype: two and one had A2063G and A2064G mutations, respectively. Fourteen of the 15 strains were subtyped: half had subtype 1 and half had subtype 2. Eight strains underwent MLVA profiling: one each had the J, A, and Z type. The remainder was unclassifiable. Conclusions. This novel discovery of macrolide-resistant M. pneumoniae strains in adults with CAP in Italy suggests that there may be increasing circulation of these strains in the population. To facilitate rapid optimization of the antibiotic strategy in Italy, macrolide resistance should be monitored by a surveillance system that is based on molecular methods.

scholarly journals Can 15-Locus Mycobacterial Interspersed Repetitive Unit-Variable-Number Tandem Repeat Analysis Provide Insight into the Evolution of Mycobacterium tuberculosis?

2005 ◽  
Vol 71 (12) ◽  
pp. 8207-8213 ◽  
Author(s):  
Andrea Gibson ◽  
Timothy Brown ◽  
Lucy Baker ◽  
Francis Drobniewski
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Tandem Repeats ◽  
Variable Number Tandem Repeat ◽  
Epidemiological Studies ◽  
Variable Number ◽  
Molecular Techniques ◽  
Nucleotide Polymorphisms ◽  
East African ◽  
Phylogeny And Evolution ◽  
Phylogenetic Lineages

ABSTRACT The phylogeny and evolution of the bacterium Mycobacterium tuberculosis is still poorly understood despite the application of a variety of molecular techniques. We analyzed 469 M. tuberculosis and 49 Mycobacterium bovis isolates to evaluate if the mycobacterial interspersed repetitive units-variable-number tandem repeats (MIRU-VNTR) commonly used for epidemiological studies can define the phylogeny of the M. tuberculosis complex. This population was characterized by previously identified silent single-nucleotide polymorphisms (sSNPs) or by a macroarray based on these sSNPs that was developed in this study. MIRU-VNTR phylogenetic codes capable of differentiating between phylogenetic lineages were identified. Overall, there was 90.9% concordance between the lineages of isolates as defined by the MIRU-VNTR and sSNP analyses. The MIRU-VNTR phylogenetic code was unique to M. bovis and was not observed in any M. tuberculosis isolates. The codes were able to differentiate between different M. tuberculosis strain families such as Beijing, Delhi, and East African-Indian. Discrepant isolates with similar but not identical MIRU-VNTR codes often displayed a stepwise trend suggestive of bidirectional evolution. A lineage-specific panel of MIRU-VNTR can be used to subdivide each lineage for epidemiological purposes. MIRU-VNTR is a valuable tool for phylogenetic studies and could define an evolutionarily uncharacterized population of M. tuberculosis complex organisms.

scholarly journals Multi-laboratory validation study of multilocus variable-number tandem repeat analysis (MLVA) for Salmonella enterica serovar Enteritidis, 2015

2017 ◽  
Vol 22 (9) ◽  
Author(s):  
Tansy Peters ◽  
Sophie Bertrand ◽  
Jonas T Björkman ◽  
Lin T Brandal ◽  
Derek J Brown ◽  
...  
Keyword(s):  
North America ◽  
Tandem Repeat ◽  
Validation Study ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
European Economic Area ◽  
The European Union ◽  
Salmonella Enterica Serovar Enteritidis ◽  
Typing Method ◽  
Repeat Analysis

Multilocus variable-number tandem repeat analysis (MLVA) is a rapid and reproducible typing method that is an important tool for investigation, as well as detection, of national and multinational outbreaks of a range of food-borne pathogens. Salmonella enterica serovar Enteritidis is the most common Salmonella serovar associated with human salmonellosis in the European Union/European Economic Area and North America. Fourteen laboratories from 13 countries in Europe and North America participated in a validation study for MLVA of S. Enteritidis targeting five loci. Following normalisation of fragment sizes using a set of reference strains, a blinded set of 24 strains with known allele sizes was analysed by each participant. The S. Enteritidis 5-loci MLVA protocol was shown to produce internationally comparable results as more than 90% of the participants reported less than 5% discrepant MLVA profiles. All 14 participating laboratories performed well, even those where experience with this typing method was limited. The raw fragment length data were consistent throughout, and the inter-laboratory validation helped to standardise the conversion of raw data to repeat numbers with at least two countries updating their internal procedures. However, differences in assigned MLVA profiles remain between well-established protocols and should be taken into account when exchanging data.

Interleukin-1 cluster combined genotype and restenosis after balloon angioplasty

2003 ◽  
Vol 90 (09) ◽  
pp. 491-500 ◽  
Author(s):  
Rodrig Marculescu ◽  
Wolfgang Mlekusch ◽  
Markus Exner ◽  
Schila Sabeti ◽  
Stefanie Michor ◽  
...  
Keyword(s):  
Interleukin 1 ◽  
Variable Number Tandem Repeat ◽  
Transluminal Angioplasty ◽  
Variable Number ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Reactive Protein ◽  
Amyloid A ◽  
Dose Dependent ◽  
Percutaneous Transluminal

SummaryThe interleukin-1 system is fundamentally involved in the pathogenesis of restenosis after percutaneous transluminal angioplasty (PTA). In order to further define the clinical impact of genetic variation in this potent proinflammatory pathway we investigated the joint effects of two single nucleotide polymorphisms in the interleukin-1 beta gene [IL-1B(–511) and IL-1B(+3954)] and a variable number tandem repeat polymorphism in intron 2 of the interleukin 1 receptor antagonist gene (IL-1RN VNTR) on postintervention inflammation and occurrence of restenosis in 183 consecutive patients who underwent successful femoropopliteal PTA. C-reactive protein (CRP) and serum amyloid A (SAA) were determined pre- and 48 hours postintervention. Patients were followed up to 12 months for the occurrence of postangioplasty restenosis (≥50 %). When analyzed separately, none of the polymorphisms was associated either with inflammation or restenosis. However, when the IL-1B (–511) and the IL-1RN VNTR genotypes were combined, a highly significant relationship was observed: Non-carriers of the two repeat allele of the IL-1RN VNTR (IL-1RN*2) who were heterozygous and homozygous for the IL-1B (–511)T allele exhibited a gradually increased inflammatory response and a higher restenosis risk. In contrast, carriers of the IL-1RN*2 and the IL-1B (–511)T allele showed a significantly better outcome.This remarkable gene dose-dependent association emphasizes the advantage of considering combinations of genetic markers rather that isolated polymorphisms in the analysis of multifactorial vascular disease.

scholarly journals A severe gastroenteritis outbreak of Salmonella enterica serovar Enteritidis PT8, with PFGE profile XbaI.0024 and MLVA profile 2-9-7-3-2 following a christening reception, Greece, 2016

2017 ◽  
Vol 146 (1) ◽  
pp. 28-36 ◽  
Author(s):  
G. MANDILARA ◽  
C. M. VASSALOS ◽  
A. CHRISOSTOMOU ◽  
K. KARADIMAS ◽  
E. MATHIOUDAKI ◽  
...  
Keyword(s):  
Salmonella Enterica ◽  
Virulent Strain ◽  
Phage Type ◽  
Variable Number Tandem Repeat ◽  
Admission Rate ◽  
Variable Number ◽  
Molecular Techniques ◽  
Contributing Factors ◽  
Salmonella Enterica Serovar Enteritidis ◽  
Hospital Admission Rate

SUMMARYIn June 2016, a Salmonella enterica serovar Enteritidis outbreak (n = 56) occurred after a christening reception in Central Greece, mainly affecting previously healthy adults; one related death caused media attention. Patients suffered from profuse diarrhoea, fever and frequent vomiting episodes requiring prolonged hospitalisation and sick leave from work, with a 54% hospital admission rate. The majority of cases experienced serious illness within <12 h of attending the party. We investigated the outbreak to identify the source(s) of infection and contributing factors to the disease severity. From the retrospective cohort study, the cheesy penne pasta was the most likely vehicle of infection (relative risk 7·8; 95% confidence interval 3·6–16·8), explaining 79% of the cases. S. enterica ser. Enteritidis isolates were typed as phage-type PT8, pulsed-field gel electrophoresis type XbaI.0024, multiple locus variable-number tandem repeat analysis-type 2-9-7-3-2. The strain did not share the single-nucleotide polymorphism address of the concurrent European S. enterica ser. Enteritidis PT8 outbreak clusters. Following five consecutive years with no documented S. enterica ser. Enteritidis outbreaks in Greece, this outbreak, likely associated with a virulent strain, prompted actions towards the enhancement of the national Salmonella molecular surveillance and control programmes including the intensification of training of food handlers for preventing similar outbreaks in the future. Advanced molecular techniques were useful in distinguishing unrelated outbreak strains.

scholarly journals Multiple-locus variable-number tandem-repeat analysis of Streptococcus pneumoniae and comparison with multiple loci sequence typing

2012 ◽  
Vol 12 (1) ◽  
pp. 241 ◽  
Author(s):  
Hélène van Cuyck ◽  
Bruno Pichon ◽  
Philippe Leroy ◽  
Alexandra Granger-Farbos ◽  
Anthony Underwood ◽  
...  
Keyword(s):  
Streptococcus Pneumoniae ◽  
Tandem Repeat ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Multiple Locus ◽  
Repeat Analysis ◽  
Multiple Loci

scholarly journals Current advances in molecular subtyping using multilocus variable number of tandem repeat analysis of Salmonella Enteritidis and Salmonella Typhimurium in Egyptian chickens

2020 ◽  
Vol 13 (10) ◽  
pp. 2252-2259
Author(s):  
Wafaa M. M. Hassan ◽  
Ashraf A. Abd El Tawab ◽  
Sara M. El-Shannat
Keyword(s):  
Salmonella Typhimurium ◽  
Tandem Repeat ◽  
Disease Transmission ◽  
Salmonella Enteritidis ◽  
Profile Analysis ◽  
Variable Number Tandem Repeat ◽  
Allelic Diversity ◽  
Variable Number ◽  
Valuable Insight ◽  
Repeat Analysis

Aim: This study aimed to characterize the genetic diversity, evolutionary level, and prevalence of genotypes of common isolates of Salmonella (Salmonella Enteritidis and Salmonella Typhimurium). Using one of the most advanced molecular recognition techniques, multilocus variable number of tandem repeat analysis (MLVA), we characterized the genotype and prevalence of S. Enteritidis and S. Typhimurium. Materials and Methods: One hundred and twenty-five internal organ samples were collected from the major chicken slaughterhouses in Egypt, and Salmonella species were isolated. PCR was utilized to amplify the IE-1 and Flic-C genes to identify S. Enteritidis and S. Typhimurium DNA, respectively, from Salmonella isolates. MLVA was applied on nine samples of S. Enteritidis DNA and three samples of S. Typhimurium DNA. Six variable number tandem repeat (VNTR) loci (Sal02, Sal04, Sal06, Sal10, Sal20, and Sal23) were amplified. Results: Of the examined samples (n=125), a total of 12 isolates (9.6%) were either identified as Enteritidis or Typhimurium. PCR-mediated amplification of IE-1 and Flic-C revealed that 75% (n=9) of the 12 Salmonella isolates were S. Enteritidis and 25% (n=3) were S. Typhimurium. The six loci amplified through MLVA had allelic diversity. The most discriminatory heterogenic locus for S. Enteritidis was Sal20. Sal04 and Sal23 were the most discriminatory heterogenic loci for S. Typhimurium. VNTR allelic profile analysis revealed nine unique genotypes for S. Enteritidis and three for S. Typhimurium. Conclusion: This study was the first to use MLVA analysis to identify S. Enteritidis and S. Typhimurium strains isolated from chickens in Egypt. The molecular typing data reported herein allowed us to characterize the genotypes of S. Enteritidis and S. Typhimurium that are most prevalent in Egyptian chickens. Moreover, this epidemiological information provides valuable insight on how to prevent disease transmission. Moreover, our methods provide an alternative to traditional serotyping techniques that may produce inaccurate strain identifications for organisms with rough lipopolysaccharide structures.

scholarly journals Prevalence and Characterization of Heterogeneous Variable-Number Tandem-Repeat Clusters Comprising Drug-Susceptible and/or Variable ResistantMycobacterium tuberculosisComplex Isolates in the Netherlands from 2004 to 2016

2018 ◽  
Vol 56 (11) ◽  
Author(s):  
Inge Roof ◽  
Rana Jajou ◽  
Miranda Kamst ◽  
Arnout Mulder ◽  
Albert de Neeling ◽  
...  
Keyword(s):  
The Netherlands ◽  
Tandem Repeat ◽  
Variable Number Tandem Repeat ◽  
Multivariate Logistic Regression Analysis ◽  
Variable Number ◽  
Linkage Data ◽  
Nucleotide Polymorphisms ◽  
Typing Method ◽  
Content Type ◽  
Heterogeneous Clustering

ABSTRACTThe variable-number tandem-repeat (VNTR) typing method is used to study tuberculosis (TB) transmission. Clustering ofMycobacterium tuberculosisisolates with identical VNTR patterns is assumed to reflect recent transmission. Hence, clusters are thought to be homogeneous regarding antibiotic resistance. In practice, however, heterogeneous clusters are also identified. This study investigates the prevalence and characteristics of heterogeneous VNTR clusters and assesses whether isolates in these clusters remain clustered when subjected to whole-genome sequencing (WGS). In the period from 2004 to 2016, 9,072 isolates were included. Demographic and epidemiological linkage data were obtained from the Netherlands Tuberculosis Register. VNTR clusters were defined as homogeneous when isolates shared identical resistance profiles or as heterogeneous if both susceptible and (variable) resistant isolates were found. Multivariate logistic regression analysis was performed to identify factors associated with heterogeneous clustering. Isolates from 2016 were subjected to WGS, and a genetic distance of 12 single nucleotide polymorphisms (SNPs) was used as the cutoff for WGS clustering. In total, 4,661/9,072 (51%) isolates were clustered into 985 different VNTR clusters, of which 217 (22%) were heterogeneous. Patient characteristics associated with heterogeneous clustering were non-Dutch ethnicity (odds ratio [OR], 1.46 [95% confidence interval {CI}, 1.22 to 1.75]), asylum seeker (OR, 1.51 [95% CI, 1.24 to 1.85]), extrapulmonary TB (OR, 1.26 [95% CI, 1.09 to 1.46]), previous TB diagnosis (OR, 1.38 [95% CI, 1.04 to 1.82]), and not being a contact of a TB patient (OR, 1.35 [95% CI, 1.08 to 1.69]). With WGS, 34% of heterogeneous and 78% of homogeneous isolates from 2016 remained clustered. Heterogeneous VNTR clusters are common but seem to be explained by a substantial degree of false clustering by VNTR typing compared to WGS.

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