scholarly journals Comparison of Conventional Molecular and Whole-Genome Sequencing Methods for Differentiating Salmonella enterica serovar Schwarzengrund Isolates Obtained from Food and Animal Sources

2021 ◽  
Vol 9 (10) ◽  
pp. 2046
Author(s):  
I-Chen Li ◽  
Rayean Wu ◽  
Chung-Wen Hu ◽  
Keh-Ming Wu ◽  
Zeng-Weng Chen ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Salmonella Enterica ◽  
Multidrug Resistant ◽  
Whole Genome ◽  
Strain Typing ◽  
Genome Wide ◽  
The Us ◽  
Typing Methods ◽  
The Cost

Over the last decade, Salmonella enterica serovar Schwarzengrund has become more prevalent in Asia, Europe, and the US with the simultaneous emergence of multidrug-resistant isolates. As these pathogens are responsible for many sporadic illnesses and chronic complications, as well as outbreaks over many countries, improved surveillance is urgently needed. For 20 years, pulsed-field gel electrophoresis (PFGE) has been the gold standard for determining bacterial relatedness by targeting genome-wide restriction enzyme polymorphisms. Despite its utility, recent studies have reported that PFGE results correlate poorly with that of closely related outbreak strains and clonally dominant endemic strains. Due to these concerns, alternative amplification-based molecular methods for bacterial strain typing have been developed, including clustered regular interspaced short palindromic repeats (CRISPR) and multilocus sequence typing (MLST). Furthermore, as the cost of sequencing continues to decrease, whole genome sequencing (WGS) is poised to replace other molecular strain typing methods. In this study, we assessed the discriminatory power of PFGE, CRISPR, MLST, and WGS methods to differentiate between 23 epidemiologically unrelated S. enterica serovar Schwarzengrund isolates collected over an 18-year period from distinct locations in Taiwan. The discriminatory index (DI) of each method for different isolates was calculated, resulting in values between 0 (not discriminatory) and 1 (highly discriminatory). Our results showed that WGS has the greatest resolution (DI = 0.982) compared to PFGE (DI = 0.938), CRISPR (DI = 0.906), and MLST (DI = 0.463) methods. In conclusion, the WGS typing approach was shown to be the most sensitive for S. enterica serovar Schwarzengrund fingerprinting.

scholarly journals Characterization and whole genome sequencing of closely related multidrug-resistant Salmonella enterica serovar Heidelberg isolates from imported poultry meat in the Netherlands

PLoS ONE ◽  
2019 ◽  
Vol 14 (7) ◽  
pp. e0219795 ◽  
Author(s):  
Redmar R. van den Berg ◽  
Serge Dissel ◽  
Michel L. B. A. Rapallini ◽  
Coen C. van der Weijden ◽  
Ben Wit ◽  
...  
Keyword(s):  
The Netherlands ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Salmonella Enterica ◽  
Multidrug Resistant ◽  
Poultry Meat ◽  
Whole Genome

scholarly journals Whole-Genome Sequencing for Outbreak Investigations of Methicillin-Resistant Staphylococcus aureus in the Neonatal Intensive Care Unit: Time for Routine Practice?

2015 ◽  
Vol 36 (7) ◽  
pp. 777-785 ◽  
Author(s):  
Taj Azarian ◽  
Robert L. Cook ◽  
Judith A. Johnson ◽  
Nilmarie Guzman ◽  
Yvette S. McCarter ◽  
...  
Keyword(s):  
Intensive Care Unit ◽  
Staphylococcus Aureus ◽  
Phylogenetic Analysis ◽  
Intensive Care ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Neonatal Intensive Care ◽  
Whole Genome ◽  
Genome Wide ◽  
Typing Methods

BACKGROUNDInfants in the neonatal intensive care unit (NICU) are at increased risk for methicillin-resistant Staphylococcus aureus (MRSA) acquisition. Outbreaks may be difficult to identify due in part to limitations in current molecular genotyping available in clinical practice. Comparison of genome-wide single nucleotide polymorphisms (SNPs) may identify epidemiologically distinct isolates among a population sample that appears homogenous when evaluated using conventional typing methods.OBJECTIVETo investigate a putative MRSA outbreak in a NICU utilizing whole-genome sequencing and phylogenetic analysis to identify recent transmission events.DESIGNClinical and surveillance specimens collected during clinical care and outbreak investigation.PATIENTSA total of 17 neonates hospitalized in a 43-bed level III NICU in northeastern Florida from December 2010 to October 2011 were included in this study.METHODSWe assessed epidemiological data in conjunction with 4 typing methods: antibiograms, PFGE, spa types, and phylogenetic analysis of genome-wide SNPs.RESULTSAmong the 17 type USA300 isolates, 4 different spa types were identified using pulsed-field gel electrophoresis. Phylogenetic analysis identified 5 infants as belonging to 2 clusters of epidemiologically linked cases and excluded 10 unlinked cases from putative transmission events. The availability of these results during the initial investigation would have improved infection control interventions.CONCLUSIONWhole-genome sequencing and phylogenetic analysis are invaluable tools for epidemic investigation; they identify transmission events and exclude cases mistakenly implicated by traditional typing methods. When routinely applied to surveillance and investigation in the clinical setting, this approach may provide actionable intelligence for measured, appropriate, and effective interventions.Infect. Control Hosp. Epidemiol. 2015;36(7):777–785

scholarly journals Cost of whole genome sequencing for non-typhoidal Salmonella enterica

PLoS ONE ◽  
2021 ◽  
Vol 16 (3) ◽  
pp. e0248561
Author(s):  
Laura Ford ◽  
Kathryn Glass ◽  
Deborah A. Williamson ◽  
Vitali Sintchenko ◽  
Jennifer M. B. Robson ◽  
...  
Keyword(s):  
Public Health ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Salmonella Enterica ◽  
Cost Savings ◽  
Whole Genome ◽  
Public Health Action ◽  
Culture Independent ◽  
Health Action ◽  
Typing Methods

Background While whole genome sequencing (WGS) may be more expensive than traditional testing and polymerase chain reaction (PCR), simple cost comparisons ignore the potential for WGS to reduce the societal costs of non-typhoidal Salmonella enterica through public health action to prevent illness. Methods We determined how many cases the use of WGS data would need to prevent to be cost-equal to serotyping and MLVA, or culture independent testing based on PCR in Australia. We then examined the costs and cost-savings of current typing methods compared with WGS in outbreak scenarios. Results A median of 275 (90% CrI -55-775) or 1.9% (90% CrI -0.4%-5.4%) of notified serotyped Salmonella cases would need to be prevented for WGS to be cost-equal to current typing methods and 1,550 (90% CrI 820–2,725) or 9.6% of all notified Salmonella cases would need to be prevented to be cost-equal to PCR. WGS is likely to result in cost savings in prolonged outbreaks, where data can support earlier public health action. Conclusions Despite currently having a higher cost per isolate, routine WGS of Salmonella was no more expensive than existing typing methods or PCR where >2% of illness was averted.

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
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