A decline in the occurrence of extended-spectrum ß-lactamase-producing Escherichia coli in retail chicken meat in the UK between 2013 and 2018.

AIMS: The aim of this study was to report on the occurrence of antimicrobial resistant (AMR) Escherichia coli from retail chicken meat samples in the UK, with particular focus on AmpC and extended spectrum beta-lactamase (ESBL) production and carbapenem resistance. METHODS AND RESULTS: Methods from EU protocols were used for selective isolation of AmpC-/ESBL-producing E. coli, carbapenem-resistant E. coli and for performing minimum inhibitory concentrations. Additional work not part of EU protocols included viable counts, detection by PCR of blaCTX-M , blaOXA, blaSHV and blaTEM genes in ESBL-phenotype E. coli and screening for mcr plasmid-mediated colistin resistance. From the 313/309 retail chicken meat samples tested in 2016/2018, carbapenem or mcr plasmid-mediated colistin-resistant E. coli were not detected. For 2016/2018 chicken samples, 141/42 (45·0%/13·6%), 90/23 (28·8%/7·4%), 48/16 (15·3%/5·2%) and 3/3 (1·0%/1·0%) were positive for ESBL- and/or AmpC-, ESBL- alone AmpC- alone and AmpC+ESBL-phenotype E. coli respectively. ESBL-producing E. coli were predominantly blaCTX-M-1 . All AmpC and/or ESBL-phenotype E. coli were sensitive to colistin, ertapenem, imipenem, meropenem, temocillin and tigecycline, applying epidemiological cut-off values. CONCLUSIONS: A previous study in 2013/14 showed that 65·4% of retail chicken meat samples tested in the UK were positive for ESBL-producing (mainly CTX-M) E. coli. Since then the proportion of samples positive in the UK has dropped significantly to 7·4% in 2018. SIGNIFICANCE AND IMPACT OF THE STUDY: Significant reductions in antimicrobials used in the UK poultry meat sector between 2012 and 2016 may be linked to significant reductions in AmpC/ESBL-phenotype E. coli in retail chicken between 2013/14 and 2018.

Longitudinal study on the occurrence in pigs of colistin-resistant Escherichia coli carrying mcr-1 following the cessation of use of colistin.

AIMS: In 2015, colistin-resistant Escherichia coli and Salmonella with the mcr-1 gene were isolated from a pig farm in Great Britain. Pigs were subsequently monitored over a ~20-month period for the occurrence of mcr-1-mediated colistin resistance and the risk of mcr-1 E. coli entering the food chain was assessed. METHODS AND RESULTS: Pig faeces and slurry were cultured for colistin-resistant E. coli and Salmonella, tested for the mcr-1 gene by PCR and selected isolates were further analysed. Seventy-eight per cent of faecal samples (n = 275) from pigs yielded mcr-1 E. coli after selective culture, but in positive samples only 0·2-1·3% of the total E. coli carried mcr-1. Twenty months after the initial sampling, faecal samples (n = 59) were negative for E. coli carrying mcr-1. CONCLUSIONS: The risk to public health from porcine E. coli carrying mcr-1 was assessed as very low. Twenty months after cessation of colistin use, E. coli carrying mcr-1 was not detected in pig faeces on a farm where it was previously present. SIGNIFICANCE AND IMPACT OF THE STUDY: The results suggest that cessation of colistin use may help over time to reduce or possibly eliminate mcr-1 E. coli on pig farms where it occurs.

Atypical Morphology and Disparate Speciation in a Case of Feline Cryptococcosis.

A 6-year-old, spayed female cat was presented with acute respiratory signs and pleural effusion. Computed tomography scan revealed a large, lobulated mass effect in the ventral right hemithorax with concurrent sternal lymphadenopathy. A cytologic sample of the mass contained pyogranulomatous inflammation, necrotic material, and abundant yeast structures that lacked a distinct capsule and demonstrated rare pseudohyphal forms. Fungal culture and biochemical testing identified the yeast as Cryptococcus albidus, with susceptibility to all antifungal agents tested. However, subsequent 18S PCR identified 99% homology with a strain of Cryptococcus neoformans and only 92% homology with C. albidus. The patient responded well to fluconazole therapy unlike the only known previous report of C. albidus in a cat. The unusual cytologic morphology in this case underscores the need for ancillary testing apart from microscopy for fungal identification. Though C. albidus should be considered as a potential feline pathogen, confirmation with PCR is recommended when such rare non-neoformans species are encountered.

Investigation of prevalence and risk factors for Campylobacter in broiler flocks at slaughter: results from a UK survey.

During 2007-2009 a UK-wide, 3-year stratified randomized survey of UK chicken broiler flocks was conducted to estimate the prevalence of Campylobacter-infected batches of birds at slaughter. Thirty-seven abattoirs, processing 88·3% of the total UK slaughter throughput, were recruited at the beginning of the survey. Of the 1174 slaughter batches sampled, 79·2% were found to be colonized with Campylobacter, the majority of isolates being C. jejuni. Previous partial depopulation of the flock [odds ratio (OR) 5·21], slaughter in the summer months (categorized as June, July and August; OR 14·27) or autumn months (categorized as September, October and November; OR 1·70) increasing bird age (40-41 days, OR 3·18; 42-45 days, OR 3·56; ⩾46 days, OR 13·43) and higher recent mortality level in the flock (1·00-1·49% mortality, OR 1·57; ⩾1·49% mortality, OR 2·74) were all identified as significant risk factors for Campylobacter colonization of the birds at slaughter. Time in transit to the slaughterhouse of more than 2·5 h was identified as a protective factor (OR 0·52).

The prevalence of Campylobacter spp. in broiler flocks and on broiler carcases, and the risks associated with highly contaminated carcases.

A baseline survey on the prevalence of Campylobacter spp. in broiler flocks and Campylobacter spp. on broiler carcases in the UK was performed in 2008 in accordance with Commission Decision 2007/516/EC. Pooled caecal contents from each randomly selected slaughter batch, and neck and breast skin from a single carcase were examined for Campylobacter spp. The prevalence of Campylobacter in the caeca of broiler batches was 75·8% (303/400) compared to 87·3% (349/400) on broiler carcases. Overall, 27·3% of the carcases were found to be highly contaminated with Campylobacter (≥1000 c.f.u./g). Slaughter in the summer months (June, July, August) [odds ratio (OR) 3·50], previous partial depopulation of the flock (OR 3·37), and an increased mortality at 14 days (≥1·25% to <1·75%) (OR 2·54) were identified as significant risk factors for the most heavily Campylobacter-contaminated carcases. Four poultry companies and farm location were also found to be significantly associated with highly contaminated carcases.

Investigation of risk factors for Salmonella on fattening-turkey farms.

A cross-sectional study into risk factors for Salmonella was undertaken using data gathered from 252 fattening turkey flocks in the UK. The data was derived from the EU baseline survey conducted during 2006 and 2007, in addition to a voluntary questionnaire. Multivariate logistic regression models identified significant risk factors for Salmonella spp. and Salmonella Typhimurium. A decreased risk of Salmonella spp. infection was associated with a history of intestinal illness in the sampled flock (OR 0.17), the use of wood shavings as litter (OR 0.21), use of disinfectant in the cleaning process (OR 0.25), incineration of dead birds on farm (OR 0.29), seasonal production (OR 0.31), farm staff also working with cattle (OR 0.31), and the presence of pigs on neighbouring farms (OR 0.38). The risk of isolating Salmonella spp. varied according to the company from which the poults were sourced. A reduced risk of S. Typhimurium infection was associated with the use of wax blocks to control rodents (OR 0.09), using mains water (OR 0.19) and having a Salmonella test programme (OR 0.23). An increased risk of S. Typhimurium infection was associated with storage of items around the turkey house (OR 5.20), evidence of mice (OR 4.71) and a soil surface surrounding the turkey house (OR 2.70). This study therefore identifies a number of important practical measures which can be implemented by farmers and veterinarians within the turkey industry to assist in the control of salmonellosis at the farm level.

Salmonella serovars and their antimicrobial resistance in British turkey flocks in 1995 to 2006.

Serovar and antimicrobial resistance data from the scanning surveillance of British turkey flocks for Salmonella between 1995 and 2006 were analysed and compared with prevalence data from other livestock and animal feed. A total of 2753 incidents of 57 different serovars were reported. The five most prevalent serovars were Salmonella Typhimurium (20.8%), Salmonella Newport (14.7%), Salmonella Derby (10.6%), Salmonella Indiana (8.3%) and Salmonella Agona (6.4%). S. Typhimurium reports peaked in the mid- to late 1990s; this occurred in parallel with the S. Typhimurium DT104 epidemic in other livestock species. S. Enteritidis reports peaked in mid- to late 1990s, followed by a considerable decrease after 2000, which was also noted in flocks of domestic fowl. S. Newport, Salmonella Montevideo, Salmonella Senftenberg and Salmonella Binza occurred in marked clusters, indicating that they were introduced into one or more flocks at a certain time (i.e. via contaminated feed or infected 1-day-old chicks). A proportion of 43.1% of the reported Salmonella isolates were resistant to at least one antimicrobial, while 17.7% were multi-resistant. No isolates were resistant to ciprofloxacin or to the third-generation cephalosporins ceftazidime and cefotaxime. Resistance to ampicillin, chloramphenicol, streptomycin, sulphonamide compounds and tetracycline was common, and it was mainly a characteristic of S. Typhimurium DT104 compared with S. Typhimurium non-DT104 and non-S. Typhimurium isolates (P<0.001). Resistance to nalidixic acid decreased from 16.9% in 1995 to 11.8% in 2006. Nalidixic acid resistance was most frequently found in Salonella Hadar (71.4%), S. Typhimurium DT104 (30.0%), S. Newport (17.9%) and S. Typhimurium non-DT104 (11.1%).

Quantitative signal detection using spontaneous ADR reporting.

Quantitative methods are increasingly used to analyse spontaneous reports. We describe the core concepts behind the most common methods, the proportional reporting ratio (PRR), reporting odds ratio (ROR), information component (IC) and empirical Bayes geometric mean (EBGM). We discuss the role of Bayesian shrinkage in screening spontaneous reports, the importance of changes over time in screening the properties of the measures. Additionally we discuss three major areas of controversy and ongoing research: stratification, method evaluation and implementation. Finally we give some suggestions as to where emerging research is likely to lead.

The fibroblast growth factor family and mood disorders.

While there has been a great deal of interest in the role of brain-derived neurotrophic factor (BDNF) in mood disorders and/or the mode of action of antidepressants, less is known about the role of other growth factors. This paper is focused on a group of growth factors, the fibroblast growth factor (FGF) family and their potential role in mood disorders.

Trends in phage types and antimicrobial resistance of Salmonella enterica serovar Enteritidis isolated from animals in Great Britain from 1990 to 2005.

Surveillance data for Salmonella enterica serovar Enteritidis incidents and isolations from food animals in Great Britain from 1990 to 2005 were analysed to detect any trends and provide the basis for a comparison between phage types (pt) and antimicrobial sensitivity patterns in human beings and animals. During 2001 to 2005 there was a decrease in incidents involving most species except ducks. Only the numbers of incidents involving pts 6, 6a, 9b and 14b (in ducks) and pts 6a and 13a (in mammals) increased significantly during this period, whereas there were 93 per cent fewer incidents involving pt 4 than in 1990 to 2000. After adjustment for pt, the isolates from ducks were more resistant to nalidixic acid, tetracyclines and sulfonamides, and were more likely to be multiresistant than isolates from chickens. Isolates from turkeys tended to be more resistant to sulfonamides than isolates from chickens. pts 1, 5a, 6, 6a and 35 had the highest level of resistance after adjusting for species. During 2001 to 2005 there was an increase in resistance among pts 1, 6 and 7, in most cases involving nalidixic acid.

Survey of the prevalence of Salmonella on commercial broiler farms in the United Kingdom, 2005/06.

Between October 2005 and September 2006, all European Union member states were required to carry out standardised surveys of the prevalence of Salmonella in broiler flock holdings to establish baseline data from which to derive national targets for disease reduction. In the uk 382 holdings were sampled, 41 of which were positive for Salmonella, giving an estimated weighted prevalence of 10.7 per cent (95 per cent confidence interval [ci] 8.1 to 13.1 per cent). The serotype most frequently isolated was Salmonella Ohio, with a weighted prevalence of 2.2 per cent (95 per cent ci 1.2 to 3.7 per cent), followed by Salmonella Kedougou at 1.7 per cent (95 per cent ci 0.9 to 3.2 per cent). There were no isolates of Salmonella Enteritidis and only a single isolation of Salmonella Typhimurium (0.2 per cent, 95 per cent ci 0.0 to 1.6 per cent). Of the three other serotypes given top priority by the eu owing to their public health significance, Salmonella Virchow was isolated from one holding, but Salmonella Hadar and Salmonella Infantis were not detected on any of the holdings.

Novel statistical tools for monitoring the safety of marketed drugs.

Robust tools for monitoring the safety of marketed therapeutic products are of paramount importance to public health. In recent years, innovative statistical approaches have been developed to screen large post-marketing safety databases for adverse events (AEs) that occur with disproportionate frequency. These methods, known variously as quantitative signal detection, disproportionality analysis, or safety data mining, facilitate the identification of new safety issues or possible harmful effects of a product. In this article, we describe the statistical concepts behind these methods, as well as their practical application to monitoring the safety of pharmaceutical products using spontaneous AE reports. We also provide examples of how these tools can be used to identify novel drug interactions and demographic risk factors for adverse drug reactions. Challenges, controversies, and frontiers for future research are discussed.

Quasiperiodicity and chaos in cardiac fibrillation.

In cardiac fibrillation, disorganized waves of electrical activity meander through the heart, and coherent contractile function is lost. We studied fibrillation in three stationary forms: in human chronic atrial fibrillation, in a stabilized form of canine ventricular fibrillation, and in fibrillation-like activity in thin sheets of canine and human ventricular tissue in vitro. We also created a computer model of fibrillation. In all four studies, evidence indicated that fibrillation arose through a quasiperiodic stage of period and amplitude modulation, thus exemplifying the "quasiperiodic transition to chaos" first suggested by Ruelle and Takens. This suggests that fibrillation is a form of spatio-temporal chaos, a finding that implies new therapeutic approaches.

Survey of the prevalence of Salmonella species on commercial laying farms in the United Kingdom.

A survey of salmonella infection on 454 commercial layer flock holdings in the uk was carried out between October 2004 and September 2005. Fifty-four (11.7 per cent, 95 per cent confidence interval 9.3 to 14.0 per cent) were salmonella positive. The most common serovar identified was Salmonella Enteritidis at a prevalence of 5.8 per cent, and 70 per cent of these isolates were phage types 4, 6, 7 and 35. Salmonella Typhimurium was the second most prevalent serovar, found in 1.8 per cent of the farms. Of the three other serovars given top priority by the eu because of their public health significance, Salmonella Virchow and Salmonella Infantis were each isolated from one holding, but Salmonella Hadar was not isolated from any of the holdings. Analysis of antimicrobial resistance patterns revealed that over 76 per cent of the isolates were sensitive to all of the 16 drugs tested, and all the isolates were sensitive to ciprofloxacin, gentamicin, ceftazidime, apramycin, amikacin, amoxicillin/clavulanic acid, neomycin and cefotaxime.

Improving dideoxynucleotide-triphosphate utilisation by the hyper-thermophilic DNA polymerase from the archaeon Pyrococcus furiosus.

Polymerases from the Pol-I family which are able to efficiently use ddNTPs have demonstrated a much improved performance when used to sequence DNA. A number of mutations have been made to the gene coding for the Pol-II family DNA polymerase from the archaeon Pyrococcus furiosus with the aim of improving ddNTP utilisation. 'Rational' alterations to amino acids likely to be near the dNTP binding site (based on sequence homologies and structural information) did not yield the desired level of selectivity for ddNTPs. However, alteration at four positions (Q472, A486, L490 and Y497) gave rise to variants which incorporated ddNTPs better than the wild type, allowing sequencing reactions to be carried out at lowered ddNTP:dNTP ratios. Wild-type Pfu-Pol required a ddNTP:dNTP ratio of 30:1; values of 5:1 (Q472H), 1:3 (L490W), 1:5 (A486Y) and 5:1 (Y497A) were found with the four mutants; A486Y representing a 150-fold improvement over the wild type. A486, L490 and Y497 are on analpha-helix that lines the dNTP binding groove, but the side chains of the three amino acids point away from this groove; Q472 is in a loop that connects this alpha-helix to a second long helix. None of the four amino acids can contact the dNTP directly. Therefore, the increased selectivity for ddNTPs is likely to arise from two factors: (i) small overall changes in conformation that subtly alter the nucleotide triphosphate binding site such that ddNTPs become favoured; (ii) interference with a conformational change that may be critical both for the polymerisation step and discrimination between different nucleotide triphosphates.

Risk factors associated with the salmonella status of dairy farms in England and Wales.

Between October 1999 and February 2001 the salmonella status of 449 dairy farms in England and Wales was determined by environmental sampling on up to four occasions. Data were collected through interview-based questionnaires, and multivariable analyses were used to identify risk factors associated with the farms either being Salmonella positive (prevalence data) or becoming Salmonella positive (incidence data). Region, herd size, month of visit and the lack of a clean visitor parking area were significantly associated with the prevalence of Salmonella species, and there was a significant trend towards an increased risk in late summer and autumn. The introduction of six- to 24-month-old cattle into a herd was associated with a reduced prevalence, but the introduction of adult cattle only, or calves with other cattle, was associated with an increased (but not significant) risk of farms being Salmonella positive. Month of visit, the lack of a clean visitor parking area, the use of part-time workers and not feeding calves whole milk, but not region or herd size, were associated with an increased incidence of salmonella.

High dose oral amiodarone loading: electrophysiologic effects and clinical tolerance.

Although amiodarone is an effective drug for the treatment of life-threatening ventricular arrhythmias, no standard oral loading dose protocol has been defined, and patients often undergo prolonged hospitalization for amiodarone loading. High dose (greater than 1,800 mg/day) oral loading has usually been reserved for unstable patients with incessant ventricular tachyarrhythmias. The current study was designed to 1) examine the clinical and electrophysiologic effects of a high dose oral amiodarone loading regimen in more stable patients; and 2) ascertain its safety and tolerance, possibly allowing shortened amiodarone loading periods and potentially decreased length of hospital stay. The study group included 16 patients with a history of recurrent ventricular arrhythmias and decreased left ventricular function, who were refractory to prior antiarrhythmic drug therapy. The oral loading protocol was 50 mg/kg per day of amiodarone for 3 days, then 30 mg/kg per day for 2 days, followed by maintenance therapy of 300 to 400 mg twice daily. Electrophysiologic testing was performed at baseline, on days 1 and 5 and during week 6. Amiodarone and desethylamiodarone levels were measured and symptoms monitored. Clinically, the high dose loading protocol was well tolerated in 15 of the 16 patients. Arrhythmias were rendered noninducible by day 1 in three patients and remained noninducible throughout the study period in two of the three. The remaining patients continued to have inducible ventricular tachycardia. Ventricular tachycardia cycle length and right ventricular effective refractory period both progressively increased significantly over baseline, starting on day 1. The 15 patients who remained in the study had no significant side effects during the loading period.(ABSTRACT TRUNCATED AT 250 WORDS)

Mechanism and cleavage specificity of the H-N-H endonuclease colicin E9.

Colicin endonucleases and the H-N-H family of homing enzymes share a common active site structural motif that has similarities to the active sites of a variety of other nucleases such as the non-specific endonuclease from Serratia and the sequence-specific His-Cys box homing enzyme I-PpoI. In contrast to these latter enzymes, however, it remains unclear how H-N-H enzymes cleave nucleic acid substrates. Here, we show that the H-N-H enzyme from colicin E9 (the E9 DNase) shares many of the same basic enzymological characteristics as sequence-specific H-N-H enzymes including a dependence for high concentrations of Mg2+ or Ca2+ with double-stranded substrates, a high pH optimum (pH 8-9) and inhibition by monovalent cations. We also show that this seemingly non-specific enzyme preferentially nicks double-stranded DNA at thymine bases producing 3'-hydroxy and 5'-phosphate termini, and that the enzyme does not cleave small substrates, such as dinucleotides or nucleotide analogues, which has implications for its mode of inhibition in bacteria by immunity proteins. The E9 DNase will also bind single-stranded DNA above a certain length and in a sequence-independent manner, with transition metals such as Ni2+ optimal for cleavage but Mg2+ a poor cofactor. Ironically, the H-N-H motif of the E9 DNase although resembling the zinc binding site of a metalloenzyme does not support zinc-mediated hydrolysis of any DNA substrate. Finally, we demonstrate that the E9 DNase also degrades RNA in the absence of metal ions. In the context of current structural information, our data show that the H-N-H motif is an adaptable catalytic centre able to hydrolyse nucleic acid by different mechanisms depending on the substrate and metal ion regime.

Persistence of Salmonella Typhimurium DT120 in abattoir paddocks holding sheep.

In the summer of 1999 there was an outbreak of Salmonella Typhimurium DT120 in people in the north of England which was unusual in being sensitive to antimicrobial drugs. The outbreak was linked to mutton and lamb from a local abattoir, and attention focused on four holding paddocks used to retain sheep before slaughter. In November 1999, samples of soil and faeces were taken from these paddocks and samples of faeces were taken from the concrete race leading from them. Salmonella Typhimurium was isolated from 59 of the 100 samples. Between January 2000 and October 2000 seven visits were made to the abattoir at each of which 100 samples were taken from the paddocks and concrete race and examined for the presence of Salmonella. The paddocks remained heavily contaminated with S Typhimurium DT120 until April when there was a marked reduction in the recovery of the organism. By June the contamination was minimal and by August it had disappeared, and the organism was not recovered in September or October.

Prevalence, incidence and geographical distribution of serovars of Salmonella on dairy farms in England and Wales.

A study of randomly selected dairy farms in England and Wales was made between October 1999 and February 2001 to estimate the prevalence and incidence of Salmonella serovars. The farms were enrolled through five milk-buying companies, which represented 63 per cent of the dairy farms in England and Wales, and they were sampled on up to four occasions (449 farms at visit 1, 272 farms at visit 2, 251 farms at visit 3 and 243 farms at visit 4). In total, 19,296 samples of pooled faecal pats and slurry were collected. The farm-specific prevalence of all serovars of Salmonella ranged from 12.1 per cent (95 per cent confidence interval [CI] 8.2 to 16.0 per cent) to 24.7 per cent (95 per cent CI 19.4 to 30.1 per cent) at each visit. The most common serovars identified were Salmonella Dublin (3.7 to 6.6 per cent farm-specific prevalence at each visit), Salmonella Agama (1.8 to 7.6 per cent) and Salmonella Typhimurium (2.6 to 4.1 per cent) The prevalence varied by region and month of sampling and increased in late summer. The incidence rate of all serovars of Salmonella was 0.43 (95 per cent CI 0.34 to 0.54) cases per farm-year at risk. There was no significant difference between the incidence rates of the common serovars S Typhimurium (0.07), S Dublin (0.06) and S Agama (0.13). A total of 29 Salmonella serovars were isolated. Few of the isolates were resistant to the 16 antimicrobial agents tested, except the isolates of S Typhimurium dt104, of which 67.9 per cent were resistant to at least five of them.