Whole genome sequencing reveals an outbreak of Salmonella Enteritidis associated with reptile feeder mice in the United Kingdom, 2012-2015

Kanagarajah, Sanch; Waldram, Alison; Dolan, Gayle P.; Jenkins, Claire; Ashton, Philip; Martín, Antonio Isidro Carrión; Davies, Robert; Frost, Andrew; Dallman, Timothy J.; Pinna, Elizabeth M. de; Hawker, Jeremy; Grant, Kathie; Elson, Richard

doi:10.1016/j.fm.2017.04.005

Cited by 47 publications

(52 citation statements)

References 23 publications

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“…Between 2013 and 2016, market research panel control groups were used in five investigations of diverse national outbreaks of gastrointestinal pathogens after observed increases in cases of: (study A) Salmonella Mikawasima with no clear excess among defined age or gender groups and no hypothesised exposures associated with illness identified from trawling questionnaires [2]; (study B) Shiga toxin-producing Escherichia coli (STEC) O157 with no clear excess among defined age or gender groups and handling or consumption of potatoes, root vegetables, tomatoes, apples or bananas identified as hypothesised exposures associated with illness [3]; (study C) Salmonella Enteritidis 5 single nucleotide polymorphism (SNP) single linkage cluster (methods for defining SNP profiles have been described previously [4]) with an excess observed among children and exposure to reptiles, particularly snakes, identified as hypothesised exposures associated with illness [5]; (study D) Cryptosporidium parvum IIdA24G1 with an excess observed among adult females and consumption of pre-prepared sandwiches with specific fillings, food bought from branches of two supermarkets and one coffee shop chain, specific dairy products or consumption and/or handling of specified salad vegetables identified as hypothesised exposures associated with illness [6]; and (study E) STEC O157 PT34 with an excess observed among adult females and consumption of salad vegetables, bagged salad, food purchased from a specific supermarket chain and salad items from catering premises identified as hypothesised exposures associated with illness [6] (Table 1). …”

Section: Methodsmentioning

confidence: 99%

Online market research panel members as controls in case–control studies to investigate gastrointestinal disease outbreaks: early experiences and lessons learnt from the UK

Mook

McCormick²,

Kanagarajah³

et al. 2018

Epidemiol. Infect.

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Established methods of recruiting population controls for case–control studies to investigate gastrointestinal disease outbreaks can be time consuming, resulting in delays in identifying the source or vehicle of infection. After an initial evaluation of using online market research panel members as controls in a case–control study to investigate a Salmonella outbreak in 2013, this method was applied in four further studies in the UK between 2014 and 2016. We used data from all five studies and interviews with members of each outbreak control team and market research panel provider to review operational issues, evaluate risk of bias in this approach and consider methods to reduce confounding and bias. The investigators of each outbreak reported likely time and cost savings from using market research controls. There were systematic differences between case and control groups in some studies but no evidence that conclusions on the likely source or vehicle of infection were incorrect. Potential selection biases introduced by using this sampling frame and the low response rate are unclear. Methods that might reduce confounding and some bias should be balanced with concerns for overmatching. Further evaluation of this approach using comparisons with traditional methods and population-based exposure survey data is recommended.

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Section: Methodsmentioning

confidence: 99%

Online market research panel members as controls in case–control studies to investigate gastrointestinal disease outbreaks: early experiences and lessons learnt from the UK

Mook

McCormick²,

Kanagarajah³

et al. 2018

Epidemiol. Infect.

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“…However, human clinical disease associated with exposure to raw‐fed pets and their food is likely to occur as sporadic and isolated cases rather than in outbreaks. Therefore, such cases typically will not feature prominently, or at all, in public health reports (Finley et al , American Veterinary Medical Association ), unless in the context of a wider outbreak (CDC ).Outbreak investigations have been conducted for human salmonellosis cases relating to a contaminated dry dog food manufacturing plant (Behravesh et al ) and to the use of frozen “feeder rodents” for pet reptiles (Cartwright et al , Kanagarajah et al ). These provide firm supportive evidence for the zoonotic risk of feeding Salmonella ‐contaminated products to pets, and in the investigation by Behravesh et al (), the risk to young children appeared to be disproportionately high.…”

Section: Risks Of Raw Feedingmentioning

confidence: 99%

“…Outbreak investigations have been conducted for human salmonellosis cases relating to a contaminated dry dog food manufacturing plant (Behravesh et al 2010) and to the use of frozen "feeder rodents" for pet reptiles (Cartwright et al 2016, Kanagarajah et al 2018). These provide firm supportive evidence for the zoonotic risk of feeding Salmonella-contaminated products to pets, and in the investigation by Behravesh et al (2010), the risk to young children appeared to be disproportionately high.…”

Section: Canadamentioning

confidence: 99%

Raw diets for dogs and cats: a review, with particular reference to microbiological hazards

Davies

Lawes

Wales

2019

J of Small Animal Practice

115

100

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There is a recent trend to feed pet dogs and cats in Britain and other developed countries on raw meat and animal by‐products using either commercial preparations or home recipes. This shift from heat‐treated processed food has been driven by perceived health benefits to pets and a suspicion of industrially produced pet food. The diets of wild‐living related species have been used as a rationale for raw feeding, but differences in biology and lifestyle impose limitations on such comparisons. Formal evidence does exist for claims by raw‐feeding proponents of an altered intestinal microbiome and (subjectively) improved stool quality. However, there is currently neither robust evidence nor identified plausible mechanisms for many of the wide range of other claimed benefits. There are documented risks associated with raw feeding, principally malnutrition (inexpert formulation and testing of diets) and infection affecting pets and/or household members. Surveys in Europe and North America have consistently found Salmonella species in a proportion of samples, typically of fresh‐frozen commercial diets. Another emerging issue concerns the risk of introducing antimicrobial‐resistant bacteria. Raw pet food commonly exceeds hygiene thresholds for counts of Enterobacteriaceae. These bacteria often encode resistance to critically important antibiotics such as extended‐spectrum cephalosporins, and raw‐fed pets create an elevated risk of shedding such resistant bacteria. Other infectious organisms that may be of concern include Listeria, shiga toxigenic E scherichia coli , parasites such as Toxoplasma gondii and exotic agents such as the zoonotic livestock pathogen Brucella suis, recently identified in European Union and UK raw pet meat imported from Argentina.

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“…WGS is increasingly replacing the current phenotypic and genotypic reference methods including serotyping, phage typing, pulsed-field gel electrophoresis (PFGE), multilocus variable-number tandemrepeat analysis (MLVA) and multilocus sequence typing (MLST) (Kanagarajah et al, 2018;Ribot and Hise, 2016). Although PFGE has proved an invaluable tool for outbreak surveillance for > 20 years (Ribot and Hise, 2016), it does have limitations.…”

Section: Discriminatory Potential Of Wgs and Comparison To Conventionmentioning

confidence: 99%

Whole genome sequencing and metagenomics for outbreak investigation, source attribution and risk assessment of food‐borne microorganisms

Koutsoumanis¹,

Allende²,

Álvarez‐Ordóñez³

et al. 2019

EFS2

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This Opinion considers the application of whole genome sequencing (WGS) and metagenomics for outbreak investigation, source attribution and risk assessment of food-borne pathogens. WGS offers the highest level of bacterial strain discrimination for food-borne outbreak investigation and sourceattribution as well as potential for more precise hazard identification, thereby facilitating more targeted risk assessment and risk management. WGS improves linking of sporadic cases associated with different food products and geographical regions to a point source outbreak and can facilitate epidemiological investigations, allowing also the use of previously sequenced genomes. Source attribution may be favoured by improved identification of transmission pathways, through the integration of spatial-temporal factors and the detection of multidirectional transmission and pathogenhost interactions. Metagenomics has potential, especially in relation to the detection and characterisation of non-culturable, difficult-to-culture or slow-growing microorganisms, for tracking of hazard-related genetic determinants and the dynamic evaluation of the composition and functionality of complex microbial communities. A SWOT analysis is provided on the use of WGS and metagenomics for Salmonella and Shigatoxin-producing Escherichia coli (STEC) serotyping and the identification of antimicrobial resistance determinants in bacteria. Close agreement between phenotypic and WGSbased genotyping data has been observed. WGS provides additional information on the nature and localisation of antimicrobial resistance determinants and on their dissemination potential by horizontal gene transfer, as well as on genes relating to virulence and biological fitness. Interoperable data will play a major role in the future use of WGS and metagenomic data. Capacity building based on harmonised, quality controlled operational systems within European laboratories and worldwide is essential for the investigation of cross-border outbreaks and for the development of international standardised risk assessments of food-borne microorganisms.

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Whole genome sequencing reveals an outbreak of Salmonella Enteritidis associated with reptile feeder mice in the United Kingdom, 2012-2015

Cited by 47 publications

References 23 publications

Online market research panel members as controls in case–control studies to investigate gastrointestinal disease outbreaks: early experiences and lessons learnt from the UK

Online market research panel members as controls in case–control studies to investigate gastrointestinal disease outbreaks: early experiences and lessons learnt from the UK

Raw diets for dogs and cats: a review, with particular reference to microbiological hazards

Whole genome sequencing and metagenomics for outbreak investigation, source attribution and risk assessment of food‐borne microorganisms

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