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• Pseudomonas aeruginosa UK strain prevalence assessed. • 51% of patients harboured either common clusters or transmissible strains. • LES prevalence remains stable (9.5%) on comparison with 2013 data. • Cross-infection with hospital-specific strains was found, but was mainly historical. We aimed to describe the UK Pseudomonas aeruginosa population structure amongst people with cystic fibrosis (PWCF), and to examine evidence for cross-infection. Variable Number Tandem Repeat (VNTR) typing was performed on 4640 isolates from 2619 PWCF received from 55 hospital laboratories between 2017 and 2019. A combination of whole genome sequence (WGS)-based analysis of four clusters from one hospital, and epidemiological analysis of shared strains in twelve hospitals evaluated cross-infection. Of 2619 PWCF, 1324 (51%) harboured common clusters or known transmissible strains, while 1295 carried unique strains/those shared among small numbers of patients. Of the former, 9.5% (250 patients) harboured the Liverpool epidemic strain (LES), followed in prevalence by clone C (7.8%; 205 patients), cluster A (5%;130 patients), and cluster D (3.6%; 94 patients). WGS analysis of 10 LES isolates, 9 of cluster D and 6 isolates each of cluster A and clone C from one hospital revealed LES formed the tightest cluster (between 7 and 205 SNPs), and cluster D the loosest (between 53 and 1531 SNPs). Hospital-specific shared strains were found in some centres, although cross-infection was largely historical, with few new acquisitions. Fifty-nine PWCF (2.3%) harboured "high-risk" clones; one ST235 isolate carried a bla IMP-1 allele. Of 2619 PWCF who had P. aeruginosa isolates submitted for VNTR, 51% harboured either common clusters or known transmissible strains, of which LES was the most common. Limited evidence of recent patient-to-patient strain transmission was found, suggesting cross-infection prevention measures and surveillance effectively reduce transmission. [ABSTRACT FROM AUTHOR]

The soaring global demand for seafood has placed unprecedented pressure on fisheries, leading to the exploitation of vulnerable marine resources and data-deficient species. Over the past few decades, a surge of molecular methods has enabled identification of traded marine animal products that may be otherwise unrecognizable through morphological analysis. While universal DNA barcoding remains a powerful authentication and traceability tool, its application still requires lengthy procedures, established facilities, and assay development. In this study, we explored some of the uses and advantages of cutting-edge nanopore sequencing, a rapid and portable alternative method. We first tested the method to identify ten opportunistically sampled fishery products obtained in two different contexts: five fish fillets marketed in the UK, four shark specimens traded in Indonesia and one fish collected as part of a scientific survey. We present a full analytical workflow to produce accurate species identification based on direct, PCR-free long-read sequencing of the DNA extracted from each specimen. We then used the nanopore sequencing output to mine whole mitogenomes from samples of varying DNA quality. Finally, we used the extensive additional genomic information produced by the sequencing to pinpoint the geographic origin of two of the identified specimens for which robust baseline data existed. In the face of increasing threats to biodiversity, and the need to control exploitation and supply of fisheries and wildlife globally, this rapid and portable approach is poised to revolutionize the monitoring of seafood supply and the trade in endangered marine wildlife, contributing to the sustainable management of aquatic resources. This infographic illustrates the process of nanopore sequencing of seafood, specimens collected from unknown locations. The process begins with the collection of seafood samples, followed by nanopore sequencing whole genome sequencing, which is then used for three main analyses: identification of the Cytochrome Oxidase I (COI) for species identification, assembly of mitogenomes, and a bespoke analysis of provenance to determine the geographical origin of the species. Created with BioRender.com. [Display omitted] • Seafood demand increases species exploitation. Nanopore sequencing aids to identify species beyond traditional means. • Nanopore sequencing offers a rapid, portable DNA barcoding alternative, tested on fish and sharks from the UK and Indonesia. • A workflow is presented species ID via direct long-read sequencing. Extracts whole mitogenomes from varied DNA quality. • Sequencing provides data on geographic origin, transforming seafood supply monitoring and promoting sustainable management. [ABSTRACT FROM AUTHOR]

Streptococcus equi. subsp. zooepidemicus (S. zooepidemicus) associated diseases in dogs have emerged as a significant concern over recent decades. S. zooepidemicus occurs sporadically in dog populations globally, with increased prevalence in shelters/kennels. This study used multilocus sequence typing (MLST) of 149 independent canine S. zooepidemicus isolates to assess associations between sequence type and breed, country of origin, disease severity, sampling type, year, and behaviour within an outbreak. No clear associations for breed, country, sampling type and year were determined in this study. ST-10 and 123 strains were present within all disease categories, from no clinical signs to severe disease. Assessment of S. zooepidemicus infection in 3 UK outbreaks at the same location found ST-10, 18, 123 strains, and a ST-173 strain in a US outbreak, were associated with haemorrhagic pneumonia and persisted in kennelled populations over time. The ST-173 clonal complex has been noted to have severe virulence capabilities in dogs and other species. S. zooepidemicus seems to thrive in environments with a high risk of transmissibility, overcrowding, stress and naïve populations, particularly for those in shelters/kennels. MLST alone cannot determine the virulence phenotype of S. zooepidemicus in dogs. However, a level of conservancy and diversity within ST allelic loci aids the opportunity to cause severe disease in dogs. Thus, further research into whole genome sequencing and characterising the virulence factors of S. zooepidemicus is warranted in dogs. • Streptococcus zooepidemicus has been isolated in outbreaks of canine pneumonia. • MLST allelic loci have been associated with varying clinical severity of disease. • ST10, ST18, ST123 and ST173 have been linked to outbreaks in kennelled dogs • MLST alone cannot determine the virulence of streptococcus zooepidemicus. [ABSTRACT FROM AUTHOR]

• In August 2020, an outbreak of Shiga toxin-producing Escherichia coli O157 occurred in the United Kingdom. • Whole genome sequencing revealed that 36 cases formed a genetically distinct cluster. • Epidemiological evidence suggested a fast-food product was a likely cause of this outbreak. In August 2020, an outbreak of Shiga toxin-producing Escherichia coli (STEC) O157:H7 occurred in the United Kingdom. Whole genome sequencing revealed that these cases formed a genetically distinct cluster. Hypotheses generated from case interviews were tested in analytical studies, and results informed environmental sampling and food chain analysis. A case–case study used non-outbreak 'comparison' STEC cases; a case–control study used a market research panel to recruit controls. A total of 36 cases were identified; all cases reported symptom onset between August 3 and August 16, 2020. The majority of cases (83%) resided in the Midlands region of England and in Wales. A high proportion of cases reported eating out, with one fast-food restaurant chain mentioned by 64% (n = 23) of cases. Both the case–case study (adjusted odds ratio (aOR) 31.8, 95% confidence interval (CI) 1.6–624.9) and the case–control study (aOR 9.19, 95% CI 1.0–82.8) revealed statistically significant results, showing that the consumption of a specific fast-food product was independently associated with infection. Consumption of a specific fast-food product was a likely cause of this outbreak. The only ingredient specific to the product was cucumbers. The supply of cucumbers was immediately halted, and no further cases have been identified. [ABSTRACT FROM AUTHOR]

Yersinia enterocolitica is an underreported cause of foodborne gastroenteritis. Little is known of the diversity of Y. enterocolitica isolated from food and which food commodities contribute to human disease. In this study, Y. enterocolitica was isolated from 37/50 raw chicken, 8/10 pork, 8/10 salmon and 1/10 leafy green samples collected at retail in the UK. Up to 10 presumptive Y. enterocolitica isolates per positive sample underwent whole genome sequencing (WGS) and were compared with publicly available genomes. In total, 207 Y. enterocolitica isolates were analyzed and belonged to 38 sequence types (STs). Up to five STs of Y. enterocolitica were isolated from individual food samples and isolates belonging to the same sample and ST differed by 0–74 single nucleotide polymorphisms (SNPs). Biotype was predicted for 205 (99 %) genomes that all belonged to biotype 1A, previously described as non-pathogenic. However, around half (51 %) of food samples contained isolates belonging to the same ST as previously isolated from UK human cases. The closest human-derived isolates shared between 17 and 7978 single nucleotide polymorphisms (SNPs) with the food isolates. Extensive food surveillance is required to determine what food sources are responsible for Y. enterocolitica infections and to re-examine the role of biotype 1A as a human pathogen. • Y. enterocolitica was isolated from chicken (74%), pork (80%), salmon (80%) and leafy green (10%) samples • Up to five Y. enterocolitica sequence types (STs) were isolated from the same food sample • Isolates from the same sample and ST differed by 0-74 single nucleotide polymorphisms (SNPs) • Almost all (99%) food Y. enterocolitica isolates were biotype 1A • Around half (51%) of food samples contained an ST previously isolated from UK human sources [ABSTRACT FROM AUTHOR]

In 2018, a T. asinigenitalis strain (MCE663) was isolated in a Persian onager tested for contagious equine metritis (CEM) in a United Kingdom (UK) zoo. This bacterium had never been reported in the UK and Multilocus Sequence Typing described a new atypically divergent ST (ST60). Although the causative agent of CEM is the bacterium Taylorella equigenitalis , a first natural outbreak of endometritis caused by T. asinigenitalis ST70 was reported in 2019, putting its pathogenic potential into question. In this context, we aimed to further sequence the T. asinigenitalis MCE663 genome and characterize the strain using phenotypical and genetic approaches. Results showed that it gathered all identification characteristics of T. asinigenitalis with smaller colonies and it was susceptible to all tested antibiotics. Genome-level phylogeny showed that the genome MCE663 formed a distinct phylogroup, and only shared ≈ 96.1% of average nucleotide identity (ANI) with the three published T. asinigenitalis genomes, which together shared ≈ 98.3% ANI. According to current cut-offs consensus for species and subspecies delineation (95% and 98%, respectively), our results support the first insights of a sublineage delineation within the T. asinigenitalis species. • Genome of a T. asinigenitalis isolated from a Persian onager in 2018 was sequenced. • This genome (MCE663) showed atypical genetic distance from those already published. • MCE663 genome analysis suggests sublineages within the T. asinigenitalis species. [ABSTRACT FROM AUTHOR]

Listeria monocytogenes is sporadically detected on a range of ready to eat fresh produce lines, such as spinach and rocket, and is a threat to public health. However, little is known about the diversity of L. monocytogenes present on fresh produce and their potential pathogenicity. In this work, fifteen Listeria monocytogenes isolates from the UK fresh produce supply chain were characterised using whole genome sequencing (WGS). Additionally, isolates were characterised based on their ability to form biofilm. Whole genome sequencing data was used to determine the sequence type of isolates based on multi-locus sequence typing (MLST), construct a core single nucleotide polymorphism (SNP) phylogeny and determine the presence of virulence and resistance associated genes. MLST revealed 9 distinct sequence types (STs) spanning 2 lineages (I & II) with one isolate belonging to the ST6 subtype, strains from which have been recently implicated in two large, food-associated L. monocytogenes outbreaks in South Africa and across Europe. Although most of the 15 isolates were different, comparison of core genome SNPs showed 4 pairs of 'indistinguishable' strains (<5 SNPs difference). Virulence profiling revealed that some isolates completely lacked the Listeria pathogenicity island-3 (LIPI-3) amongst other virulence factors. Investigation of the inlA gene showed that no strains in this study contained a premature stop codon (PMSC), an indicator of attenuated virulence. Assessment of biofilm production showed that isolates found in the fresh produce supply chain differ in their ability to form biofilm. This trait is considered important for L. monocytogenes to persist in environments associated with food production and processing. Overall the work indicates that a genetically diverse range of L. monocytogenes strains is present in the UK fresh produce supply chain and the virulence profiles found suggests that at least some of the strains are capable of causing human illness. Interestingly, the presence of some genetically indistinguishable isolates within the 15 isolates examined suggests that cross-contamination in the fresh produce environment does occur. These findings have useful implications in terms of food safety and for informing microbial surveillance programmes in the UK fresh produce supply chain. • The Lm population in the UK leafy produce supply chain is genetically diverse • Isolates are related to epidemic strains and possess the necessary genes for disease • Biofilm production differs amongst closely related isolates • WGS provides valuable information on isolates that is of interest to stakeholders [ABSTRACT FROM AUTHOR]

Fresh betel leaves (Piper betle L.), imported into the UK are a traditional ready-to-eat food consumed by Asian populations. We report here the consolidation of routinely collected data to model the public health risks from consumption of this food. Amongst 2110 samples collected at Border Inspection, wholesale, catering or retail, Salmonella was detected in 488 (23%) of samples tested between 2011 and 2017 and was the most commonly Salmonella-contaminated ready-to-eat food examined by Public Health England during this period. Using data from multiple samples (usually 5) tested per consignment sampled at Border Inspection, contamination levels were calculated by most probable number: seasonal, temporal and country specific differences were detected. Quantitative contamination data was used to estimate the levels present at retail, and a β-Poisson dose response model the probability of illness was calculated. Using data for products imported from India, the probability of acquiring infection following a single exposure (comprising of a single leaf) was estimated to be between 0.00003 (January–March) and 0.0001 (July–September). Using British Asian population data for individuals over 30 years of age in England in 2011, two estimates of consumption were modelled as 2.1 and 12.8 million servings per annum. Results from the model estimated 160 cases (range 102 to 242) and 960 cases (range 612 to 1456) per year in England for the two consumption estimates and equated to 34 (range 22 to 51) and 204 (range 130 to 310) salmonellosis cases per year reported to national surveillance. Salmonella from 475 of the contaminated samples were further characterised which showed a heterogeneous population structure with 46 S. enterica subsp. Enterica serovars, together with S. enterica subs diarizonae and salamae identified. Isolates from individual consignments were diverse and close genetic relationships between independent isolates were very rare except from within an individual consignment. There were no outbreaks detected as associated with betel leaf consumption. However analysis by whole genome sequencing of the 2014–17 data identified two cases where the clinical isolate had <5 single nucleotide polymorphism differences to isolates from betel leaves which is indicative of a likely epidemiological link and common source of contamination. Due to the diversity of the Salmonella contaminating this product, associations between salmonellosis cases and betel leaf consumption will appear sporadic and unlikely to be detected by current surveillance strategies based on outbreak detection. • Betel leaves are a ready-to-eat food imported to UK and consumed by Asian populations. • Salmonella was detected in 23% of 2110 samples collected in England during 2011–17. • WGS identified two salmonellosis cases with evidence of links to Salmonella from betel leaves. • Quantitative risk assessment was applied to assess public health risks. • Cases associated with betel leaf consumption are unlikely to be detected by current surveillance. [ABSTRACT FROM AUTHOR]

Abstract Genomic medicine is the use of sequence data from an individual's entire genetic code to aid diagnosis and personalise therapeutic options. An important goal of the 100,000 genomes project in the UK is to embed the infrastructure for the widespread use of whole genome sequencing into the National Health Service. Paediatricians will be at the forefront in using this new technology in the diagnosis of children with multiple congenital anomalies, developmental delay and other suspected genetic conditions. This article provides a description of the basic concepts of genomic medicine. The types of genomic testing that are available are discussed and examples of how genomics is already being used in paediatrics are given. Finally, the challenges for genomic medicine are summarised. [ABSTRACT FROM AUTHOR]

• SSTs in UK shellfish harvesting waters are 18–22 °C for 8 consecutive weeks. • Increasing SSTs do not necessarily drive growth of V. parahaemolyticus in shellfish. • Whole genome sequencing identifies V. rotiferianus and V. jasicida in shellfish. • V. jascinda and V. rotiferianus show pathogenicity in insect infection model. Warming sea-surface temperature has led to an increase in the prevalence of Vibrio species in marine environments. This can be observed particularly in temperate regions where conditions for their growth has become more favourable. The increased prevalence of pathogenic Vibrio species has resulted in a worldwide surge of Vibriosis infections in human and aquatic animals. This study uses sea-surface temperature data around the English and Welsh coastlines to identify locations where conditions for the presence and growth of Vibrio species is favourable. Shellfish samples collected from three locations that were experiencing an increase in sea-surface temperature were found to be positive for the presence of Vibrio species. We identified important aquaculture pathogens Vibrio rotiferianus and Vibrio jasicida from these sites that have not been reported in UK waters. We also isolated human pathogenic Vibrio species including V. parahaemolyticus from these sites. This paper reports the first isolation of V. rotiferianus and V. jasicida from UK shellfish and highlights a growing diversity of Vibrio species inhabiting British waters. [ABSTRACT FROM AUTHOR]

The use of Whole genome sequencing (WGS) identified a multi-country outbreak of human listeriosis associated with consumption of frozen sweet corn produced in Hungary. The purpose of this report was to summarise information on the cases occurring in the UK which were part of this outbreak and outline investigations on the presence of Listeria monocytogenes in the affected food chain. Prior to the international recall of this product in 2018, 12 UK cases of listeriosis were identified as infected by the outbreak strain between 2015 and 18. Epidemiological and microbiological investigations confirmed these cases as belonging to the outbreak. A further case occurred in 2019 and a contaminated frozen pack from one of the implicated batches of sweet corn was recovered from the patient's domestic freezer. The outbreak strain was also detected in products from a sandwich manufacturer in 2018 which added frozen sweet corn directly to sandwich fillings. The sandwich manufacturer's sweet corn was supplied by a distributor in England which obtained frozen products from the Hungarian manufacturer implicated in the outbreak. Within the distributor's premises, 208 food and environmental samples were taken: L. monocytogenes was detected in 44% of 70 samples of frozen sweet corn and 5% of 79 other foods. The outbreak strain was detected in the frozen sweet corn, in one other frozen food (mixed vegetables) and in the factory environment. The outbreak strain was also recovered from frozen beans on retail sale in the first four months of 2019. Five other L. monocytogenes strains together with two other Listeria species were detected in samples from the importer's premises. One of the L. monocytogenes strains in the importer's factory, which was distinct from the outbreak strain, was also recovered from sweet corn collected from the sandwich manufacturer, sweet corn tested in England in 2013 and 2016 and the blood of two cases of human listeriosis which occurred in England in 2014. This report shows how analysis by WGS provides evidence to understand complex food chains. This report also highlights risks for transmission of human listeriosis from frozen sweet corn and the potential for misuse of this food as a ready-to-eat product. • A multi-country listeriosis outbreak was associated with Hungarian sweet corn. • 12 cases were detected in the UK between 2015 and 2018. • Contaminated sweet corn was recovered from the freezer of a further case in 2019. • At the importer, 44% of sweet corn were contaminated, 6 strains were recovered. • A second possible sweet corn outbreak of two cases was detected. [ABSTRACT FROM AUTHOR]

Genome sequencing (GS) will have a profound impact on the diagnosis of rare and inherited diseases in children and young people. We conducted 27 semi-structured interviews with young people aged 11–19 having GS through the UK 100, 000 Genomes Project. Participants demonstrated an understanding of the role and function of genes and DNA, however the terms 'genome' and 'genome sequencing' were less well understood. Participants were primarily motivated to take part to get a diagnosis or identify the gene causing their condition. The majority of participants understood they might not receive a diagnostic result. Most were unconcerned about data security or access, however anxieties existed around what the results might show and the potential for disappointment if the result was negative. Signing an assent form empowered young people, formalised the process and instilled a sense of responsibility for their choice to participate. Most young people (≥16 years) had consented to receive secondary findings and had come to that decision without parental influence. Our research suggests that at least some young people are capable of making informed decisions about taking part in GS, and that involving them in discussions about testing can empower them to take responsibility over healthcare decisions that affect them. [ABSTRACT FROM AUTHOR]

Globally, V. parahaemolyticus is the most prevalent food-poisoning bacterium associated with seafood consumption. To date, the epidemiology of Vibrio parahaemolyticus infections in the UK has remained unexplored. Here we analysed archived V. parahaemolyticus strains isolated from domestic infections and travellers into the UK from 2008 to 2018 and who had submitted clinical samples to Public Health England (PHE)'s Gastrointestinal Bacteria Reference Unit. A total of 48 strains were retrieved from the PHE strain collection, confirmatory tested by PCR and analysed by genome-wide phylogeny using a global collection of genomes with representative strains from the major epidemic clones. Most reported infections entering the UK originated from travellers returning from Southeast Asia, however cases were also reported to have potentially originated from the USA, Cuba, India, Turkey, Caribbean, France, Slovenia and also within the UK, highlighting the wide geographical spread of infections. A large genetic diversity of V. parahaemolyticus strains was observed, with sequence type 3 (ST3; pandemic group) strains the most common sequence type (23 of the 48 analysed strains, 47.9%). The majority of strains were tdh positive (25/48, 71%), with 5 isolates positive for both haemolysin genes (tdh and trh), with 2 isolates trh positive only (5.7%). Six isolates did not possess either haemolysin gene. We demonstrate that whole genome sequencing can be effective to type certain human pathogens entering a traditionally considered "non-endemic" county and this was captured via passive epidemiological surveillance systems. Such approaches may potentially provide a useful snapshot of the diversity of a given pathogen group circulating worldwide. • Little data is currently available on pathogenic Vibrio in non-endemic regions. • This study provides insights of Vibrio parhaemolyticus strains entering the UK. • Pandemic isolates (sequence type 3) predominate cases entering back into the UK. • A number of novel and new sequence types were also identified from this study. • Study outlines the use of passive surveillance for studying foodborne pathogens. [ABSTRACT FROM AUTHOR]

Background The 100,000 Genomes Project aims to improve cancer care for NHS patients in the UK through personalised medicine. Our target is to return WGS results to clinicians in a clinically meaningful timescale to facilitate diagnosis and treatment choices for patients, and in parallel to provide a research platform of genomic data linked to longitudinal clinical data. Methods We present here an overview of clinical utility for reported outcomes. To date, bioinformatics reports for WGS, with links to potentially relevant therapies and UK clinical trials, have been produced for more than 14,000 cancer patients in the UK Currently our bioinformatics analysis of WGS includes clinical interpretation of somatic small variants, somatic structural and copy number variants (SV/CNV), germline pertinent findings, mutational burden and signatures. To iteratively develop a high-quality bioinformatics pipeline and to monitor clinical utility of returned results, we are collecting feedback via the 100,000 Genomes Project Interpretation Portal from NHS Molecular Tumour Boards. These data suggest that WGS has the potential to affect patient management. Future applications will include the utilisation of pan-genomic markers to better stratify patients within the context of a clinical study. Results WGS has the ability to replace multiple standard of care tests as it has the potential to detect all types of variants (SV/CNV/SNV/indels) as well as emerging pan-genome biomarkers in a single test. In this study we use samples submitted as part of the 100,000 Genomes Project to investigate the feasibility of WGS as an alternative to conventional testing. Overall comparison of WGS with the results of NGS panels (96 patients, 156 clinically-relevant SNVs), high-depth exome sequencing (10 patients, 3150 SNVs, 140 indels), cytogenetic FISH tests (70 patients, 259 SVs, 100 CNVs), immunohistochemistry tests for Mismatch Repair Deficiency (265 patients) and HER2 status (154 patients) demonstrated Positive Percentage Agreement > 90% and False Positive Rate < 5%. Conclusions Further work is required to validate fully all aspects of the WGS analysis pipeline but these results indicate that WGS can reliably detect clinically relevant biomarkers in the genomes of cancer patients. Legal entity responsible for the study Genomics England. Funding Genomics England. Disclosure All authors have declared no conflicts of interest. [ABSTRACT FROM AUTHOR]