The Transformation of Reference Microbiology Methods and Surveillance for Salmonella With the Use of Whole Genome Sequencing in England and Wales

Chattaway, Marie Anne; Dallman, Timothy J.; Larkin, Lesley; Nair, Satheesh; McCormick, Jacquelyn; Mikhail, Amy; Hartman, Hassan; Godbole, Gauri; Powell, D. G.; Day, Martin; Smith, Robert; Grant, Kathie

doi:10.3389/fpubh.2019.00317

Cited by 79 publications

(105 citation statements)

References 45 publications

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“…In this study, we used ODC2 - clusters of isolates with no more than 2 allele differences at MGT9 level- to detect potential outbreak clusters and to assess whether some STs were more likely to cause large outbreak clusters, based on the number of ODC2 clusters and the total number of isolates in these clusters in different STs. Since the global data may be biased towards outbreak isolates that were preferentially sequenced, we used UK data from 2014 to 2018 which included all human isolates referred to public health authorities [21]. There were 17 ODC2 clusters of more than 50 isolates representing 1855 isolates in total.…”

Section: Resultsmentioning

confidence: 99%

“…Since the global data may be biased towards outbreak isolates that were preferentially sequenced, we used UK data from 2014 which included all human isolates in that year in their collection [20]. At MGT4, there were 17 ODC2 clusters of more than 50 isolates representing 1855 isolates in total, 88% of which belonged to 12 different MGT4-STs ( Supplementary Table S5).…”

Section: Detection Of Potential Large Outbreak Clusters Of S Enteritmentioning

confidence: 99%

“…The lack of potential source isolates within MGT4-CC1 STs highlights the need for comprehensive sequencing and epidemiological efforts across the food chain.Temporal variation of UK S. Enteritidis was depicted clearly by MGT, showcasing the power of MGT for longer term epidemiology. From 2014, all clinical S. Enteritidis were routinely sequenced in the UK[20]. Some MGT5-STs were found to occur for a few months and then disappeared.…”

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confidence: 99%

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Elucidation of global and local genomic epidemiology ofSalmonella entericaserovar Enteritidis through multilevel genome typing

Luo

Payne

Kaur

et al. 2020

Preprint

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AbstractSalmonella Enteritidis is a major foodborne pathogen that causes both local and international outbreaks with complex transmission pathways. Invasive infections which are associated with multidrug resistance are an increasing concern around the globe. However, the global epidemiological picture of S. Enteritidis remains unclear due to the lack of a fine scale typing scheme based on genomic sequencing data. Here, using the novel multilevel genome typing (MGT) approach, we have characterised the genomic epidemiology of S. Enteritidis in unpreceded detail. We examined 26,670 publicly available S. Enteritidis whole genome sequences from 86 countries over 101 years to reveal their spatial and temporal distributions. Using MGT4 and MGT5, we identified globally prevalent and regionally restricted STs. Source associated STs were identified, such as poultry associated MGT4-STs, which were common in human cases in the USA. Temporal trends were observed in the UK with MGT5-STs from 2014 to 2018, revealing both long lived endemic STs and the rapid expansion of new STs. Using MGT3 to MGT6, we identified MDR associated STs to facilitate tracking MDR spread. The majority of the global S. Enteritidis population fell within two predominant lineages with significant differences in geographic distribution, outbreak frequency, antimicrobial resistance and mutation rate. An online open MGT database has been established for unified international surveillance of S. Enteritidis. We demonstrated that MGT provides a flexible and high-resolution genome typing tool for S. Enteritidis surveillance and outbreak detection.

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Section: Resultsmentioning

confidence: 99%

Section: Detection Of Potential Large Outbreak Clusters Of S Enteritmentioning

confidence: 99%

mentioning

confidence: 99%

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Elucidation of global and local genomic epidemiology ofSalmonella entericaserovar Enteritidis through multilevel genome typing

Luo

Payne

Kaur

et al. 2020

Preprint

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“…For example, in the UK all Salmonella isolates are routinely sequenced, but not all S. aureus isolates. 73 74 Prioritisation should be guided by what are the most urgent local public health concerns and associated research questions. Cost-effectiveness also plays a role in the decision on what isolates to sequence.…”

Section: How Can Barriers To Implementing Wgs Surveillance In Lmics Bmentioning

confidence: 99%

Whole-genome sequencing as part of national and international surveillance programmes for antimicrobial resistance: a roadmap

2020

BMJ Glob Health

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The global spread of antimicrobial resistance (AMR) and lack of novel alternative treatments have been declared a global public health emergency by WHO. The greatest impact of AMR is experienced in resource-poor settings, because of lack of access to alternative antibiotics and because the prevalence of multidrug-resistant bacterial strains may be higher in low-income and middle-income countries (LMICs). Intelligent surveillance of AMR infections is key to informed policy decisions and public health interventions to counter AMR. Molecular surveillance using whole-genome sequencing (WGS) can be a valuable addition to phenotypic surveillance of AMR. WGS provides insights into the genetic basis of resistance mechanisms, as well as pathogen evolution and population dynamics at different spatial and temporal scales. Due to its high cost and complexity, WGS is currently mainly carried out in high-income countries. However, given its potential to inform national and international action plans against AMR, establishing WGS as a surveillance tool in LMICs will be important in order to produce a truly global picture. Here, we describe a roadmap for incorporating WGS into existing AMR surveillance frameworks, including WHO Global Antimicrobial Resistance Surveillance System, informed by our ongoing, practical experiences developing WGS surveillance systems in national reference laboratories in Colombia, India, Nigeria and the Philippines. Challenges and barriers to WGS in LMICs will be discussed together with a roadmap to possible solutions.

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“…Whole-genome sequencing (WGS) analysis of bacterial pathogens is increasingly used globally by public health institutions to investigate foodborne disease outbreaks [8][9][10]. However, in Africa, WGS activities for foodborne outbreak investigations is lagging behind.…”

Section: Introductionmentioning

confidence: 99%

Whole-genome sequencing to investigate two concurrent outbreaks of Salmonella Enteritidis in South Africa, 2018

Smith

Tau

Ngomane

et al. 2020

Journal of Medical Microbiology

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Salmonella enterica serotype Enteritidis ( Salmonella Enteritidis) is a major cause of foodborne disease outbreaks worldwide. In 2018, two concurrent outbreaks of Salmonella Enteritidis gastroenteritis in one district of South Africa were investigated. We describe the use of whole-genome sequencing (WGS) analysis of bacterial isolates to assist with the investigation of these outbreaks. Outbreak A affected children (n=27) attending a day-care centre, while outbreak B affected adults (n=16) who ate breakfast at the same restaurant. Salmonella Enteritidis was isolated from stool samples in both outbreaks (four children in outbreak A; 12 restaurant customers and three restaurant food-handlers in outbreak B). In outbreak B, Salmonella Enteritidis was isolated from three food retention samples (raw chicken egg, hollandaise sauce and rocket-herb). Available isolates from both outbreaks (n=13) were investigated using WGS analysis. Sequencing data for isolates were analysed at the EnteroBase web-based platform and included core-genome multi-locus sequence typing (cgMLST). Isolates with epidemiological links to the restaurant (n=10) and day-care centre (n=3), were shown by cgMLST to be highly genetically related, with no more than five allele differences when comparing one isolate against another. On food history, eggs and hollandaise sauce were the common food items consumed by ill restaurant customers. Unfortunately, Salmonella Enteritidis isolated from the egg and hollandaise sauce were not available for WGS analysis. Our investigation concluded that the two concurrent outbreaks were caused by a highly related strain of Salmonella Enteritidis, suggesting the possibility of a common contaminated food source, of which contaminated eggs are strongly implicated.

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The Transformation of Reference Microbiology Methods and Surveillance for Salmonella With the Use of Whole Genome Sequencing in England and Wales

Cited by 79 publications

References 45 publications

Elucidation of global and local genomic epidemiology ofSalmonella entericaserovar Enteritidis through multilevel genome typing

Elucidation of global and local genomic epidemiology ofSalmonella entericaserovar Enteritidis through multilevel genome typing

Whole-genome sequencing as part of national and international surveillance programmes for antimicrobial resistance: a roadmap

Whole-genome sequencing to investigate two concurrent outbreaks of Salmonella Enteritidis in South Africa, 2018

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