Epidemiological characterization and phylogenetic analysis of the emerging Salmonella enterica serovar Napoli: the first cause of invasive nontyphoidal salmonellosis in Lombardy, northern Italy

2016 ◽  
Author(s):  
Maria Gori
Keyword(s):  
Phylogenetic Analysis ◽  
Salmonella Enterica ◽  
Northern Italy ◽  
First Cause ◽  
Epidemiological Characterization

scholarly journals Draft Genome Sequences of 40 Salmonella enterica Serovar Typhimurium Strains Isolated from Humans and Food in Brazil: TABLE 1 

2016 ◽  
Vol 4 (5) ◽  
Author(s):  
Fernanda Almeida ◽  
Marta Inês Cazentini Medeiros ◽  
Dália Prazeres Rodrigues ◽  
Justin Payne ◽  
Ruth E. Timme ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Health Problem ◽  
Salmonella Enterica ◽  
Salmonella Enterica Serovar Typhimurium ◽  
Draft Genome ◽  
Genome Sequences ◽  
Serovar Typhimurium ◽  
Important Health

Salmonellosis is an important health problem worldwide and Salmonella enterica serovar Typhimurium is one of the most common isolated serovars. Here, we reported the draft genomes of 40 S . Typhimurium strains isolated from humans and food in Brazil. These draft genomes will improve phylogenetic analysis and will help enhance our understanding of strains of this serovar isolated in Brazil.

scholarly journals First records of the North American leafhopper Gyponana mail (Hemiptera: Cicadellidae) invading urban gardens and agroecosystems in Europe

2021 ◽  
pp. 213-219
Author(s):  
Valeria Trivellone ◽  
Vally Forte ◽  
Luisa Filippin ◽  
Christopher H. Dietrich
Keyword(s):  
Phylogenetic Analysis ◽  
Host Plant ◽  
North American ◽  
Male Genitalia ◽  
Morphological Study ◽  
European Population ◽  
Northern Italy ◽  
Urban Gardens ◽  
The North ◽  
Palearctic Region

The Nearctic leafhopper species Gyponana (Gyponana) mali DeLong, 1942 is reported from Europe for the fi rst time and represents the fi rst record of the tribe Gyponini Stål, 1870 (Hemiptera: Cicadellidae: Iassinae: Gyponini) for the Palearctic Region. Specimens were collected in southern Switzerland (Ticino) and two regions of northern Italy (Lombardy and Veneto) in 2015–2019. The preferred host plant in these areas appears to be Cornus sanguinea L. Phylogenetic analysis of the COI barcode sequences grouped one of the European specimens with three individuals of G. (G.) mali from Ontario, Canada. Morphological study indicated that the male genitalia of the European population are intermediate between G. (G.) mali and G. (G.) extenda DeLong, 1942.

scholarly journals Usefulness of High-Quality Core Genome Single-Nucleotide Variant Analysis for Subtyping the Highly Clonal and the Most Prevalent Salmonella enterica Serovar Heidelberg Clone in the Context of Outbreak Investigations

2015 ◽  
Vol 54 (2) ◽  
pp. 289-295 ◽  
Author(s):  
S. Bekal ◽  
C. Berry ◽  
A. R. Reimer ◽  
G. Van Domselaar ◽  
G. Beaudry ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Salmonella Enterica ◽  
Core Genome ◽  
Phage Type ◽  
Epidemiological Data ◽  
Single Nucleotide Variant ◽  
High Quality ◽  
Typing Method ◽  
Single Nucleotide ◽  
Content Type

Salmonella entericaserovar Heidelberg is the second most frequently occurring serovar in Quebec and the third-most prevalent in Canada. Given that conventional pulsed-field gel electrophoresis (PFGE) subtyping for commonSalmonellaserovars, such asS. Heidelberg, yields identical subtypes for the majority of isolates recovered, public health laboratories are desperate for new subtyping tools to resolve highly clonalS. Heidelberg strains involved in outbreak events. As PFGE was unable to discriminate isolates from three epidemiologically distinct outbreaks in Quebec, this study was conducted to evaluate whole-genome sequencing (WGS) and phylogenetic analysis as an alternative to conventional subtyping tools. Genomes of 46 isolates from 3 Quebec outbreaks (2012, 2013, and 2014) supported by strong epidemiological evidence were sequenced and analyzed using a high-quality core genome single-nucleotide variant (hqSNV) bioinformatics approach (SNV phylogenomics [SNVphyl] pipeline). Outbreaks were indistinguishable by conventional PFGE subtyping, exhibiting the same PFGE pattern (SHEXAI.0001/SHEBNI.0001). Phylogenetic analysis based on hqSNVs extracted from WGS separated the outbreak isolates into three distinct groups, 100% concordant with the epidemiological data. The minimum and maximum number of hqSNVs between isolates from the same outbreak was 0 and 4, respectively, while >59 hqSNVs were measured between 2 previously indistinguishable outbreaks having the same PFGE and phage type, thus corroborating their distinction as separate unrelated outbreaks. This study demonstrates that despite the previously reported high clonality of this serovar, the WGS-based hqSNV approach is a superior typing method, capable of resolving events that were previously indistinguishable using classic subtyping tools.

Molecular Characterization and Phylogenetic Analysis of Enteroviruses and Hepatitis A Viruses in Sewage Samples, Northern Italy, 2016

2019 ◽  
Vol 11 (4) ◽  
pp. 393-399
Author(s):  
Laura Pellegrinelli ◽  
Cristina Galli ◽  
Sandro Binda ◽  
Valeria Primache ◽  
Catia Tagliacarne ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Molecular Characterization ◽  
Hepatitis A ◽  
Northern Italy

scholarly journals Ongoing large measles outbreak with nosocomial transmission in Milan, northern Italy, March–August 2017

2017 ◽  
Vol 22 (33) ◽  
Author(s):  
Antonella Amendola ◽  
Silvia Bianchi ◽  
Elena R Frati ◽  
Giulia Ciceri ◽  
Marino Faccini ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Rapid Analysis ◽  
Northern Italy ◽  
Nosocomial Transmission ◽  
Phylogenetic Data ◽  
Measles Outbreak ◽  
Sporadic Cases ◽  
Surrounding Areas ◽  
Transmission Pathways

A large measles outbreak has been ongoing in Milan and surrounding areas. From 1 March to 30 June 2017, 203 measles cases were laboratory-confirmed (108 sporadic cases and 95 related to 47 clusters). Phylogenetic analysis revealed the co-circulation of two different genotypes, D8 and B3. Both genotypes caused nosocomial clusters in two hospitals. The rapid analysis of epidemiological and phylogenetic data allowed effective surveillance and tracking of transmission pathways.

scholarly journals Genomic diversity of Salmonella enterica isolated from papaya samples collected during multiple outbreaks in 2017

Microbiology ◽  
2020 ◽  
Vol 166 (5) ◽  
pp. 453-459
Author(s):  
Arthur W. Pightling ◽  
James Pettengill ◽  
Yan Luo ◽  
Errol Strain ◽  
Hugh Rand
Keyword(s):  
Phylogenetic Analysis ◽  
Drug Administration ◽  
Salmonella Enterica ◽  
Type Species ◽  
Food And Drug Administration ◽  
Genomic Diversity ◽  
Diverse Populations ◽  
Content Type ◽  
The Us ◽  
Geographic Regions

In 2017, the US Food and Drug Administration investigated the sources of multiple outbreaks of salmonellosis. Epidemiologic and traceback investigations identified Maradol papayas as the suspect vehicles. During the investigations, the genomes of 55 Salmonella enterica that were isolated from papaya samples were sequenced. Serovar assignments and phylogenetic analysis placed the 55 isolates into ten distinct groups, each representing a different serovar. Within-serovar SNP differences are generally between 0 and 20 SNPs, while the median between-serovar distance is 51 812 SNPs. We observed two groups with SNP distances between 21 and 100 SNPs. These relatively large within-serovar SNP distances may indicate that the isolates represent either diverse populations or multiple, genetically distinct subpopulations. Further inspection of these cases with traceback evidence allowed us to identify an 11th population. We observed that high levels of genomic diversity from individual firms is possible, with one firm yielding five of the ten serovars. Also, high levels of diversity are possible within small geographic regions, as five of the serovars were isolated from papayas that originated from farms located in Armería and Tecomán, Colima. In addition, we identified AMR genes that are present in three of the serovars studied here (aph(3’)-lb, aph(6)-ld, tet(C), fosA7, and qnrB19) and we detected the presence of the plasmid IncHI2A among S. Urbana isolates.

scholarly journals Genomic characterization and phylogenetic analysis of Salmonella enterica serovar Javiana

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10256
Author(s):  
Lauren K. Hudson ◽  
Lisha Constantine-Renna ◽  
Linda Thomas ◽  
Christina Moore ◽  
Xiaorong Qian ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Population Structure ◽  
Salmonella Enterica ◽  
Genome Wide Association Study ◽  
Phylogenetic Analyses ◽  
Branch Length ◽  
Human Infection ◽  
Clinical Isolates ◽  
Genes Encoding ◽  
Allelic Differences

Salmonella enterica serovar Javiana is the fourth most reported serovar of laboratory-confirmed human Salmonella infections in the U.S. and in Tennessee (TN). Although Salmonella ser. Javiana is a common cause of human infection, the majority of cases are sporadic in nature rather than outbreak-associated. To better understand Salmonella ser. Javiana microbial population structure in TN, we completed a phylogenetic analysis of 111 Salmonella ser. Javiana clinical isolates from TN collected from Jan. 2017 to Oct. 2018. We identified mobile genetic elements and genes known to confer antibiotic resistance present in the isolates, and performed a pan-genome-wide association study (pan-GWAS) to compare gene content between clades identified in this study. The population structure of TN Salmonella ser. Javiana clinical isolates consisted of three genetic clades: TN clade I (n = 54), TN clade II (n = 4), and TN clade III (n = 48). Using a 5, 10, and 25 hqSNP distance threshold for cluster identification, nine, 12, and 10 potential epidemiologically-relevant clusters were identified, respectively. The majority of genes that were found to be over-represented in specific clades were located in mobile genetic element (MGE) regions, including genes encoding integrases and phage structures (91.5%). Additionally, a large portion of the over-represented genes from TN clade II (44.9%) were located on an 87.5 kb plasmid containing genes encoding a toxin/antitoxin system (ccdAB). Additionally, we completed phylogenetic analyses of global Salmonella ser. Javiana datasets to gain a broader insight into the population structure of this serovar. We found that the global phylogeny consisted of three major clades (one of which all of the TN isolates belonged to) and two cgMLST eBurstGroups (ceBGs) and that the branch length between the two Salmonella ser. Javiana ceBGs (1,423 allelic differences) was comparable to those from other serovars that have been reported as polyphyletic (929–2,850 allelic differences). This study demonstrates the population structure of TN and global Salmonella ser. Javiana isolates, a clinically important Salmonella serovar and can provide guidance for phylogenetic cluster analyses for public health surveillance and response.

scholarly journals Whole-Genome Sequence of the First Extended-Spectrum β-Lactamase-Producing Strain of Salmonella enterica subsp. enterica Serovar Napoli

2018 ◽  
Vol 7 (10) ◽  
Author(s):  
Mathieu Clément ◽  
Alban Ramette ◽  
Odette J. Bernasconi ◽  
Luigi Principe ◽  
Francesco Luzzaro ◽  
...  
Keyword(s):  
Pediatric Patient ◽  
Genome Sequence ◽  
Salmonella Enterica ◽  
Northern Italy ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Content Type ◽  
Extended Spectrum

We report here the whole-genome sequence of the first extended-spectrum β-lactamase (ESBL)-producing strain of Salmonella enterica subsp. enterica serovar Napoli, LC0541/17, isolated from the stools of an ambulatory pediatric patient in northern Italy.

scholarly journals Two New Sturgeon Species are Susceptible to Acipenser Iridovirus European (AcIV-E) Infection

Pathogens ◽  
2020 ◽  
Vol 9 (3) ◽  
pp. 156 ◽  
Author(s):  
Davide Mugetti ◽  
Paolo Pastorino ◽  
Vasco Menconi ◽  
Margherita Messina ◽  
Loretta Masoero ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Major Capsid Protein ◽  
Phylogenetic Analyses ◽  
Northern Italy ◽  
Russian Sturgeon ◽  
Economic Losses ◽  
Molecular Analyses ◽  
First Case ◽  
Sturgeon Species ◽  
Acipenser Stellatus

We report the first case of Acipenser iridovirus European (AcIV-E) infection in starry sturgeon (Acipenser stellatus) and in sterlet (A. ruthenus) reared in Northern Italy. During 2018, mortality began in A. stellatus and A. ruthenus specimens reared in co-habitation with Russian sturgeon positive for AcIV-E. Molecular analyses were done on the gills to amplify a fragment of the major capsid protein (MCP) gene using real-time PCR against AcIV-E. DNA of the positive samples was further sequenced and phylogenetic analyses were performed. The MCP gene sequences were highly similar to a virus previously identified in Italy (nucleotide identities between 99.38% and 99.69%). Phylogenetic analysis confirmed our hypothesis of passage of the virus from the infected Russian sturgeon. The detection of AcIV-E in new species of the Acipenseridae family may impact on sturgeon production, with relevant economic losses.

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