BackgroundDuring a substantial elevation in scarlet fever (SF) notifications in 2014 a national genomic study was undertaken of Streptococcus pyogenes (Group A Streptococci, GAS) isolates from patients with SF with comparison to isolates from patients with invasive disease (iGAS) to test the hypotheses that the increase in SF was due to either the introduction of one or more new/emerging strains in the population in England or the transmission of a known genetic element through the population of GAS by horizontal gene transfer (HGT) resulting in infections with an increased likelihood of causing SF. Isolates were collected to provide geographical representation, for approximately 5% SF isolates from each region from 1st April 2014 to 18th June 2014. Contemporaneous iGAS isolates for which genomic data were available were included for comparison. Data were analysed in order to determine emm gene sequence type, phylogenetic lineage and genomic clade representation, the presence of known prophage elements and the presence of genes known to confer pathogenicity and resistance to antibiotics.Results555 isolates were analysed, 303 from patients with SF and 252 from patients with iGAS. Isolates from patients with SF were of multiple distinct emm sequence types and phylogenetic lineages. Prior to data normalisation, emm3 was the predominant type (accounting for 42.9% of SF isolates, 130/303 95%CI 37.5–48.5; 14.7% higher than the percentage of emm3 isolates found in the iGAS isolates). Post-normalisation emm types, 4 and 12, were found to be over-represented in patients with SF versus iGAS (p < 0.001). A single gene, ssa, was over-represented in isolates from patients with SF. No single phage was found to be over represented in SF vs iGAS. However, a “meta-ssa” phage defined by the presence of :315.2, SPsP6, MGAS10750.3 or HK360ssa, was found to be over represented. The HKU360.vir phage was not detected yet the HKU360.ssa phage was present in 43/63 emm12 isolates but not found to be over-represented in isolates from patients with SF.ConclusionsThere is no evidence that the increased number of SF cases was a strain-specific or known mobile element specific phenomenon, as the increase in SF cases was associated with multiple lineages of GAS.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3603-z) contains supplementary material, which is available to authorized users.

During the decade to 1999, the incidence of human infections with the zoonotic pathogen verocytotoxin-producing Escherichia coli O157 (VTEC O157) increased in England and Wales. This paper describes the results of a survey of 75 farms to determine the prevalence of faecal excretion of VTEC O157 by cattle, its primary reservoir host, in England and Wales. Faecal samples were collected from 4663 cattle between June and December 1999. The prevalence of excretion by individual cattle was 4.2 per cent (95 per cent confidence interval [CI] 2.0 to 6.4) and 10.3 per cent (95 per cent CI 5.8 to 14.8) among animals in infected herds. The within-herd prevalence on positive farms ranged from 1.1 to 51.4 per cent. At least one positive animal was identified on 29 (38.7 per cent; 95 per cent CI 28.1 to 50.4) of the farms, including dairy, suckler and fattening herds. The prevalence of excretion was least in the calves under two months of age, peaked in the calves aged between two and six months and declined thereafter. The phage types identified most widely were 4, 34 and 2, which were each found on six of the 29 positive farms.

An ELISA developed to diagnose Fasciola hepatica infection in cattle by detecting serum antibodies was adapted and validated for use with samples of bulk-tank milk. The prevalence of the infection in 61 dairy herds was established by using serum antibody levels or faecal egg counts measured in a proportion of the cows in each herd. The correlation between the results of the ELISA and the herd seroprevalence was 0.83. Using a cut-off value of 27 per cent positive, the bulk-tank ELISA identified herds in which more than 25 per cent of the cows were infected with a diagnostic sensitivity of 96 per cent (95 per cent confidence interval 89 to 100 per cent) and a diagnostic specificity of 80 per cent (95 per cent confidence interval 66 to 94 per cent). By applying the ELISA to 623 herds in England and 445 herds in Wales, the prevalence of F hepatica infection in England was estimated to be 48 per cent (95 per cent confidence interval 46 to 54 per cent), and in Wales 86 per cent (95 per cent confidence interval 84 to 90 per cent).

Liver fluke (Fasciola hepatica) infection caused weight loss, diarrhoea, decreased milk yield and occasionally death in cattle in East Anglia during the winters of 2001 to 2003. The condition had previously been limited mainly to stock imported into this part of Britain from endemically infected areas. In composite faecal samples collected by 16 farm animal veterinary practices in Norfolk, Suffolk and Essex, fluke eggs were found in 15 (28.8 per cent) of 52 previously unaffected suckler herds and 10 (16.7 per cent) of 60 dairy herds. Antibodies to F hepatica were detected by elisa in 32 (53.3 per cent) of the bulk milk samples from these 60 dairy herds, including the 10 in which fluke eggs were found. The emergence of fasciolosis in East Anglia was attributed to recent higher summer rainfall, which favoured the intermediate snail host Lymnaea truncatula and the free-living stages of F hepatica, the increased influx of sheep from endemic fluke areas for seasonal grazing, and the wetter grazing conditions associated with the Environmentally Sensitive Area scheme.

An outbreak of caprine tuberculosis caused by Mycobacterium bovis was disclosed in June 2008, affecting goats of the golden Guernsey breed kept on 10 separate smallholdings in south-west Wales and the west of England. Following the initial diagnosis at postmortem examination, 30 goats that reacted positively to the single intradermal comparative cervical tuberculin (SICCT) test, together with five in-contact animals, were euthanased and subjected to postmortem examination and mycobacterial culture. Spoligotyping and variable number tandem repeat analysis of isolates showed that they were all of the same genotype, endemic to south-west Wales. Retrospective movement tracings identified a goat herd in south-west Wales, by then completely dispersed, as the probable common source of infection. There was a perfect correlation between the SICCT test and culture results in all slaughtered goats. Grossly visible tubercular lesions were observed at postmortem examination in all but one reactor.

A faecal egg count reduction test, using composite samples, was developed in order to assess the efficacy of the flukicide, triclabendazole (TCBZ) on commercial sheep farms in England and Wales. First, a comparison between individual counts and composite counts was conducted using sheep on two farms with different levels of infection. Faecal samples were collected from 50 sheep on each farm at the time of TCBZ treatment and 21 days later. The results showed that a composite fluke egg count (CFEC) was as sensitive as using individual samples, and the test was subsequently validated on an additional 18 sheep farms. The pre- and post-treatment CFECs using five composite samples were subjected to bootstrap analysis. The variance in fluke egg counts of composite samples was high, but analyses indicated that 20 individual samples analysed as two composites was as sensitive as using five composites. The two-composite assay was evaluated on another five farms. On seven out of 25 farms sampled, egg counts either did not decrease significantly or increased following treatment, suggesting TCBZ resistance on these farms. This assay represents a practical field test that can be used in the first instance to evaluate the efficacy of TCBZ on sheep farms where resistance is suspected.

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