scholarly journals Outbreak of Salmonella enterica serotype Poona in infants linked to persistent Salmonella contamination in an infant formula manufacturing facility, France, August 2018 to February 2019

2019 ◽  
Vol 24 (13) ◽  
Author(s):  
Gabrielle Jones ◽  
Maria Pardos de la Gandara ◽  
Laura Herrera-Leon ◽  
Silvia Herrera-Leon ◽  
Carmen Varela Martinez ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Infant Formula ◽  
Genome Sequencing ◽  
Salmonella Enterica ◽  
Outbreak Detection ◽  
Whole Genome ◽  
Sequencing Analysis ◽  
Manufacturing Facility

We describe a Salmonella Poona outbreak involving 31 infant cases in France. Following outbreak detection on 18 January 2019, consumption of rice-based infant formula manufactured at a facility in Spain was identified as the probable cause, leading to a recall on 24 January. Whole genome sequencing analysis linked present outbreak isolates to a 2010–11 S. Poona outbreak in Spain associated with formula manufactured in the same facility, indicating a persistent source of contamination.

Evaluation of Whole Genome Sequencing for outbreak detection of Salmonella enterica serovar Enteritidis

2020 ◽  
Author(s):  
Ainhoa Arrieta-Gisasola ◽  
Aitor Atxaerandio Landa ◽  
Javier Garaizar ◽  
Joseba Bikandi ◽  
José Karkamo ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Salmonella Enterica ◽  
Outbreak Detection ◽  
Whole Genome ◽  
Salmonella Enterica Serovar Enteritidis

scholarly journals Evaluation of Whole Genome Sequencing for Outbreak Detection of Salmonella enterica

PLoS ONE ◽  
2014 ◽  
Vol 9 (2) ◽  
pp. e87991 ◽  
Author(s):  
Pimlapas Leekitcharoenphon ◽  
Eva M. Nielsen ◽  
Rolf S. Kaas ◽  
Ole Lund ◽  
Frank M. Aarestrup
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Salmonella Enterica ◽  
Outbreak Detection ◽  
Whole Genome

scholarly journals Whole Genome Sequencing Analysis of Salmonella enterica Serovar Typhi: History and Current Approaches

2021 ◽  
Vol 9 (10) ◽  
pp. 2155
Author(s):  
Wan Ratmaazila Wan Makhtar ◽  
Izwan Bharudin ◽  
Nurul Hidayah Samsulrizal ◽  
Nik Yusnoraini Yusof
Keyword(s):  
Infectious Diseases ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Salmonella Enterica ◽  
Point Of Care ◽  
Genomic Research ◽  
Whole Genome ◽  
Sequencing Analysis ◽  
Significant Information ◽  
Salmonella Enterica Serovar Typhi

In recent years, the advance in whole-genome sequencing technology has changed the study of infectious diseases. The emergence of genome sequencing has improved the understanding of infectious diseases, which has revamped many fields, such as molecular microbiology, epidemiology, infection control, and vaccine production. In this review we discuss the findings of Salmonella enterica serovar Typhi genomes, publicly accessible from the initial complete genome to the recent update of Salmonella enterica serovar Typhi genomes, which has greatly improved Salmonella enterica serovar Typhi and other pathogen genomic research. Significant information on genetic changes, evolution, antimicrobial resistance, virulence, pathogenesis, and investigation from the genome sequencing of S. Typhi is also addressed. This review will gather information on the variation of the Salmonella enterica serovar Typhi genomes and hopefully facilitate our understanding of their genome evolution, dynamics of adaptation, and pathogenesis for the development of the typhoid point-of-care diagnostics, medications, and vaccines.

scholarly journals Whole-Genome Sequencing Analysis of Nontyphoidal Salmonella enterica of Chicken Meat and Human Origin Under Surveillance in Sri Lanka

2019 ◽  
Vol 16 (7) ◽  
pp. 531-537 ◽  
Author(s):  
Moon Y.F. Tay ◽  
Sujatha Pathirage ◽  
Lakshmi Chandrasekaran ◽  
Uddami Wickramasuriya ◽  
Nirasha Sadeepanie ◽  
...  
Keyword(s):  
Sri Lanka ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Salmonella Enterica ◽  
Chicken Meat ◽  
Whole Genome ◽  
Sequencing Analysis ◽  
Human Origin

scholarly journals Characterization of Foodborne Outbreaks of Salmonella enterica Serovar Enteritidis with Whole-Genome Sequencing Single Nucleotide Polymorphism-Based Analysis for Surveillance and Outbreak Detection

2015 ◽  
Vol 53 (10) ◽  
pp. 3334-3340 ◽  
Author(s):  
Angela J. Taylor ◽  
Victoria Lappi ◽  
William J. Wolfgang ◽  
Pascal Lapierre ◽  
Michael J. Palumbo ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Salmonella Enterica ◽  
Outbreak Detection ◽  
Whole Genome ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Molecular Subtyping ◽  
Foodborne Outbreaks

Salmonella entericaserovar Enteritidis is a significant cause of gastrointestinal illness in the United States; however, current molecular subtyping methods lack resolution for this highly clonal serovar. Advances in next-generation sequencing technologies have made it possible to examine whole-genome sequencing (WGS) as a potential molecular subtyping tool for outbreak detection and source trace back. Here, we conducted a retrospective analysis ofS. Enteritidis isolates from seven epidemiologically confirmed foodborne outbreaks and sporadic isolates (not epidemiologically linked) to determine the utility of WGS to identify outbreaks. A collection of 55 epidemiologically characterized clinical and environmentalS. Enteritidis isolates were sequenced. Single nucleotide polymorphism (SNP)-based cluster analysis of theS. Enteritidis genomes revealed well supported clades, with less than four-SNP pairwise diversity, that were concordant with epidemiologically defined outbreaks. Sporadic isolates were an average of 42.5 SNPs distant from the outbreak clusters. Isolates collected from the same patient over several weeks differed by only two SNPs. Our findings show that WGS provided greater resolution between outbreak, sporadic, and suspect isolates than the current gold standard subtyping method, pulsed-field gel electrophoresis (PFGE). Furthermore, results could be obtained in a time frame suitable for surveillance activities, supporting the use of WGS as an outbreak detection and characterization method forS. Enteritidis.

Whole-genome sequencing analysis and CRISPR genotyping of rare antibiotic-resistant Salmonella enterica serovars isolated from food and related sources

2021 ◽  
Vol 93 ◽  
pp. 103601
Author(s):  
Daniel F.M. Monte ◽  
Matthew A. Nethery ◽  
Rodolphe Barrangou ◽  
Mariza Landgraf ◽  
Paula J. Fedorka-Cray
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Salmonella Enterica ◽  
Whole Genome ◽  
Sequencing Analysis ◽  
Antibiotic Resistant

scholarly journals A common protocol for the simultaneous processing of multiple clinically relevant bacterial species for whole genome sequencing

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kathy E. Raven ◽  
Sophia T. Girgis ◽  
Asha Akram ◽  
Beth Blane ◽  
Danielle Leek ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Dna Extraction ◽  
Genome Sequencing ◽  
Clinical Microbiology ◽  
Bacterial Species ◽  
Outbreak Detection ◽  
Whole Genome ◽  
Library Preparation ◽  
Simultaneous Processing ◽  
Antimicrobial Resistance Gene

AbstractWhole-genome sequencing is likely to become increasingly used by local clinical microbiology laboratories, where sequencing volume is low compared with national reference laboratories. Here, we describe a universal protocol for simultaneous DNA extraction and sequencing of numerous different bacterial species, allowing mixed species sequence runs to meet variable laboratory demand. We assembled test panels representing 20 clinically relevant bacterial species. The DNA extraction process used the QIAamp mini DNA kit, to which different combinations of reagents were added. Thereafter, a common protocol was used for library preparation and sequencing. The addition of lysostaphin, lysozyme or buffer ATL (a tissue lysis buffer) alone did not produce sufficient DNA for library preparation across the species tested. By contrast, lysozyme plus lysostaphin produced sufficient DNA across all 20 species. DNA from 15 of 20 species could be extracted from a 24-h culture plate, while the remainder required 48–72 h. The process demonstrated 100% reproducibility. Sequencing of the resulting DNA was used to recapitulate previous findings for species, outbreak detection, antimicrobial resistance gene detection and capsular type. This single protocol for simultaneous processing and sequencing of multiple bacterial species supports low volume and rapid turnaround time by local clinical microbiology laboratories.

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