SnapperDB: A database solution for routine sequencing analysis of bacterial isolates

Dallman, Timothy J.; Ashton, Philip; Schafer, Ulf; Jironkin, Aleksey; Painset, Anaïs; Shaaban, Sharif; Hartman, Hassan; Underwood, Anthony; Jenkins, Claire; Grant, Kathie

doi:10.1101/189118

Cited by 40 publications

(50 citation statements)

References 15 publications

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“…Isolates of STEC O157:H7 with less than five SNPs differences within their core genome are considered closely related and likely to have an epidemiological link [15]. Hierarchical single linkage clustering was performed on the pairwise SNP difference between all isolates at various distance thresholds (Δ250, Δ100, Δ50, Δ25, Δ10, Δ5, Δ0) [16]. The result of the clustering is a SNP address that can be used to describe the population structure based on clonal groups.…”

Section: Microbiologymentioning

confidence: 99%

An outbreak of Shiga toxin-producing Escherichia coli O157:H7 associated with contaminated salad leaves: epidemiological, genomic and food trace back investigations

et al. 2017

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In August 2015, Public Health England detected an outbreak of Shiga toxin-producing Escherichia coli (STEC) serotype O157:H7 caused by contaminated salad leaves in a mixed leaf prepacked salad product from a national retailer. The implicated leaves were cultivated at five different farms and the zoonotic source of the outbreak strain was not determined. In March 2016, additional isolates from new cases were identified that shared a recent common ancestor with the outbreak strain. A case-case study involving the cases identified in 2016 revealed that ovine exposures were associated with illness (n = 16; AOR 8·24; 95% CI 1·55-39·74). By mapping the recent movement of sheep and lambs across the United Kingdom, epidemiological links were established between the cases reporting ovine exposures. Given the close phylogenetic relationship between the outbreak strain and the isolates from cases with ovine exposures, it is plausible that ovine faeces may have contaminated the salad leaves via untreated irrigation water or run-off from fields nearby. Timely and targeted veterinary and environmental sampling should be considered during foodborne outbreaks of STEC, particularly where ready to eat vegetables and salads are implicated.

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Section: Microbiologymentioning

confidence: 99%

An outbreak of Shiga toxin-producing Escherichia coli O157:H7 associated with contaminated salad leaves: epidemiological, genomic and food trace back investigations

et al. 2017

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“…Characterisation of isolates was performed in GBRU using a variety of methods [25][26][27][28]. Results were compared with isolates from clinical cases as part of national surveillance.…”

Section: Microbiological Examinationmentioning

confidence: 99%

Microbiological quality of raw drinking milk and unpasteurised dairy products: results from England 2013–2019

et al. 2020

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The aim of this study was to review microbiology results from testing >2500 raw drinking milk and dairy products made with unpasteurised milk examined in England between 2013 and 2019. Samples were collected as part of incidents of contamination, investigation of infections or as part of routine monitoring and were tested using standard methods for a range of both pathogens and hygiene indicators. Results from testing samples of raw cow's milk or cheese made from unpasteurised milk for routine monitoring purposes were overall of better microbiological quality than those collected during incident or investigations of infections. Results from routine monitoring were satisfactory for 62% of milks, 82% of cream, 100% of ice-cream, 51% of butter, 63% of kefir and 79% of cheeses, with 5% of all samples being considered potentially hazardous. Analysis of data from cheese demonstrated a significant association between increasing levels of indicator Escherichia coli with elevated levels of coagulase positive staphylococci and decreased probability of isolation of Shiga toxin-producing E. coli. These data highlight the public health risk associated with these products and provide further justification for controls applied to raw drinking milk and dairy products made with unpasteurised milk.

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“…Полногеномное SNP-типирование проводится по биоинформатическому алгоритму, включающему получение SNP-профилей в результате выравнивания (картирования) генома нуклеотидных прочтений каждого исследуемого изолята на полногеномную нуклеотидную последовательность референс-генома [36,37]. SNР-профили сравнивают различными методами филогенетического анализа или, наиболее часто, попарной оценкой различий в количестве SNP.…”

Section: Snp-типированиеunclassified

Modern Salmonella subtyping methods in outbreak investigations

Egorova¹,

Kuleshov²,

Кафтырева³

2019

Immunopathol Allergol Infectol

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В обзоре представлены методы молекулярного субтипирования (серотипирование, MLST, PFGE, MLVA, WGS) изолятов Salmonella spp., использующиеся в рамках эпидемиологического надзора и при расследовании случаев групповой заболеваемости сальмонеллезами. Отражена методическая основа и степень внедрения этих методов в работу лабораторий в мире. Особое внимание уделено методам субтипирования, основанным на данных полногеномного секвенирования, и существующим международным платформам для анализа данных "Pathogene Detection" и "Enterobase".

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SnapperDB: A database solution for routine sequencing analysis of bacterial isolates

Cited by 40 publications

References 15 publications

An outbreak of Shiga toxin-producing Escherichia coli O157:H7 associated with contaminated salad leaves: epidemiological, genomic and food trace back investigations

An outbreak of Shiga toxin-producing Escherichia coli O157:H7 associated with contaminated salad leaves: epidemiological, genomic and food trace back investigations

Microbiological quality of raw drinking milk and unpasteurised dairy products: results from England 2013–2019

Modern Salmonella subtyping methods in outbreak investigations

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