F A Clifton-Hadley

Nottinghamshire Healthcare NHS Trust, Nottigham, England, United Kingdom

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Publications (54)141.48 Total impact

  • [show abstract] [hide abstract]
    ABSTRACT: SUMMARY The objective of this study was to estimate the sensitivity and specificity of a culture method and a polymerase chain reaction (PCR) method for detection of two Campylobacter species: C. jejuni and C. coli. Data were collected during a 3-year survey of UK broiler flocks, and consisted of parallel sampling of caeca from 436 batches of birds by both PCR and culture. Batches were stratified by season (summer/non-summer) and whether they were the first depopulation of the flock, resulting in four sub-populations. A Bayesian approach in the absence of a gold standard was adopted, and the sensitivity and specificity of the PCR and culture for each Campylobacter subtype was estimated, along with the true C. jejuni and C. coli prevalence in each sub-population. Results indicated that the sensitivity of the culture method was higher than that of PCR in detecting both species when the samples were derived from populations infected with at most one species of Campylobacter. However, from a mixed population, the sensitivity of culture for detecting both C. jejuni or C. coli is reduced while PCR is potentially able to detect both species, although the total probability of correctly identifying at least one species by PCR is similar to that of the culture method.
    Epidemiology and Infection 03/2014; · 2.87 Impact Factor
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    ABSTRACT: Closely related bacterial isolates can display divergent phenotypes. This can limit the usefulness of phylogenetic studies for understanding bacterial ecology and evolution. Here we compare phenotyping, based on Raman spectrometric analysis of cellular composition, and phylogenetic classification by Ribosomal Multilocus Sequence Typing (rMLST) in 108 isolates of the zoonotic pathogens Campylobacter jejuni and C. coli. Automatic Relevance Determination (ARD) was used to identify informative peaks in the Raman spectra that could be used to distinguish strains in taxonomic and host source groups (species, clade, clonal complex, isolate source/host). Phenotypic characterization based on Raman spectra showed a degree of agreement with genotypic classification using rMLST, with segregation accuracy between species (83.95 %), clade (in C. coli, 98.41 %) and to some extent clonal complex (73.8 % C. jejuni ST-21 and ST-45 complexes) being achieved. This confirmed the utility of Raman spectroscopy for lineage classification and the correlation between genotypic and phenotypic classification. In parallel analysis, relatively distantly related isolates (different clonal complexes) were assigned the correct host origin irrespective of the clonal origin (74.1 - 97.0% accuracy) based upon different Raman peaks. This suggests that the phenotypic characteristics, from which the phenotypic signal is derived, are not fixed by clonal descent but are influenced by the host environment and may change as strains move between hosts.
    Applied and environmental microbiology 11/2012; · 3.69 Impact Factor
  • A B Vidal, J Rodgers, M Arnold, F Clifton-Hadley
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    ABSTRACT: Summary The objective of the study was to evaluate the performance of different combinations of sample type, transport medium and culture methods for the recovery of Campylobacter jejuni and C. coli from broiler flocks at primary production. Boot swabs moistened with one of four different transport media [maximum recovery diluent (n = 120), Exeter broth (EX) (n = 120), buffered peptone water (n = 120) and modified semi-solid Cary-Blair (n = 120)], caecal samples (n = 40) and faecal samples (n = 120) from 40 broiler flocks were compared and sensitivity estimates obtained using a Bayesian model. Samples were cultured onto mCCDA before and after enrichment in EX and incubated microaerobically at 41.5°C. Campylobacter suspect colonies were identified to the species level by multiplex PCR. Results from the Bayesian model indicated that boot swabs after enrichment had higher sensitivity (90-94%) than caecal contents before or after enrichment (84% and 89%, respectively) and faecal samples after enrichment (82%) for the detection of Campylobacter spp., although these differences were not statistically significant. Enrichment significantly increased the sensitivity of boot swab and caecal samples for detection of Campylobacter spp. and C. jejuni, respectively. However, the enrichment of caecal samples resulted in a significant decrease in the sensitivity of these samples for detection of C. coli. There was much greater variation in the sensitivity estimates of the methods for detecting C. coli than for C. jejuni, and the ranking of methods was different between the two species. Boot swabs gave the best sensitivity values for detection of C. jejuni, and enrichment culture of faecal samples was the most sensitive method for detection of C. coli.
    Zoonoses and Public Health 08/2012; · 2.09 Impact Factor
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    ABSTRACT: Salmonella in cattle herds may behave as epidemic or endemic infections. An intensive longitudinal sampling study across all management groups and ages on six dairy farms in the UK was used to examine patterns of Salmonella shedding, following the prior identification of either Salmonella Dublin (SD) (three farms) or Salmonella Typhimurium (ST) (three farms) on the premises in the context of clinical salmonellosis. Individual faeces, pooled faeces and environmental samples (total 5711 samples), taken approximately every six weeks for 15-24 weeks, were cultured for Salmonella. SD was detected at low frequency (on any visit, 0.5-18.3 per cent of samples positive) and most consistently in calves. By contrast, ST was isolated at higher frequency (on any visit, 6.8-75 per cent of samples positive), and in higher numbers, up to 10(7) cfu/g faeces. Significantly more samples from calves were positive for ST than were positive for SD (50.6 per cent v 3.1 per cent; P < 0.001), which was also true for milking cows (46.3 per cent v 4.4 per cent; P < 0.001). The differences could help to explain the different patterns of bovine infection classically associated with these two serovars in the UK. No consistent effect upon shedding was seen among the ST-infected herds following vaccination.
    The Veterinary record. 08/2012; 171(8):194.
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    ABSTRACT: 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).
    Epidemiology and Infection 05/2012; 140(10):1725-37. · 2.87 Impact Factor
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    ABSTRACT: To examine possible correlations in bovine Salmonella isolates between environmental survival and serovar-associated epidemiological patterns, bovine field isolates of Salmonella serovars Typhimurium and Dublin (two each) were inoculated into bovine faeces slurry and tested monthly by culture for survival during a six-month period of storage at a variable ambient temperature in a disused animal transporter. Low moisture conditions, where the slurry was dried onto wooden dowels, increased detectable survival of a low-level inoculum by up to five months, compared with wet slurry. A more modest increase of survival time was seen with storage of wet slurry under refrigeration at 4°C. Under both dry and wet conditions, the concentration of culturable Salmonella Typhimurium declined at a slower rate than did that of Salmonella Dublin. Salmonella that was naturally contaminating bovine faeces from farms with Salmonella Typhimurium did not show superior survival times compared with Salmonella Typhimurium that had been artificially inoculated into samples. The differing survival characteristics of the two serovars that was observed in environmental faeces may complement their different modes of infection in cattle. Salmonella Dublin, being a bovine host-adapted strain that establishes chronic infection in some animals, may have less need to survive for a prolonged period outside of its host than does Salmonella Typhimurium.
    Veterinary Microbiology 04/2012; 159(3-4):509-14. · 3.13 Impact Factor
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    ABSTRACT: Detection and enumeration of Campylobacter spp. in broiler chicken flocks are key components of research and surveillance studies aimed at reducing Campylobacter infections in people. Direct culture of caecal contents onto selective agar is the typical method used to confirm flock colonisation. Modified charcoal cefoperazone deoxycholate agar (mCCDA) is commonly used for this method, although alternative selective media have been used. Additionally, PCR methods to detect Campylobacter DNA from caecal contents may provide a rapid alternative. However comparative performance data for these methods is limited and therefore required to ensure optimal detection methods for this sample type. In this study, 306 broiler caeca were tested for Campylobacter using direct culture on mCCDA, Skirrows and Preston agars and two real-time PCR methods, one specific for mapA/ceuE regions and another for the flaA gene region. Additionally, the suitability of spread plating and spiral plating methods for enumeration of Campylobacter and the impact of sample storage were assessed. This study confirmed modified CCDA as an optimal media for detection of Campylobacter in broiler caeca. It was significantly more sensitive than Skirrows or Preston agars. This study also demonstrated that the mapA/ceuE PCR had excellent agreement with culture on mCCDA and is a genuine alternative method. Spread plating and spiral plating methods were suitable for enumeration although spiral plating appeared more sensitive for stored samples (72 h). A 1 log reduction in viable Campylobacters was observed in stored samples, therefore storage effects should be considered for quantitative studies with broiler caeca.
    Veterinary Microbiology 04/2012; 159(3-4):390-6. · 3.13 Impact Factor
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    ABSTRACT: SUMMARYA 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.
    Epidemiology and Infection 02/2012; · 2.87 Impact Factor
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    ABSTRACT: Escherichia coli O115 has been isolated from healthy sheep and was shown to be associated with attaching-effacing (AE) lesions in the large intestine. Following previous observations of interactions between E. coli O157 and O26, the aim of the present study was to assess what influence an O115 AE E. coli (AEEC) would have on E. coli O157 colonisation in vitro and in vivo. We report that E. coli O115- and O157-associated AE lesions were observed on HEp-2 cells and on the mucosa of ligated ovine spiral colon. In single strain inoculum, E. coli O115 associated intimately with HEp-2 cells and the spiral colon in greater numbers than E. coli O157:H7. However, in mixed inoculum studies, the number of E. coli O115 AE lesions was significantly reduced suggesting negative interference by E. coli O157. Use of the ligated colon model in the present work has allowed in vitro observations to be extended and confirmed whilst using a minimum of experimental animals. The findings support a hypothesis that some AEEC can inhibit adhesion of other AEEC in vivo. The mechanisms involved may prove to be of utility in the control of AE pathovars.
    Research in Veterinary Science 08/2011; 93(1):42-5. · 1.77 Impact Factor
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    ABSTRACT: This study investigated the diversity and persistence of Salmonella strains through the pork finishing cycle, from the farm into the abattoir. Isolates from four batches of finishers, from farm to abattoir, were used. Salmonella Typhimurium isolates were subjected to molecular typing using pulsed-field gel electrophoresis and variable number of tandem repeat analysis. The results demonstrated that infection was transferred from the farm to the abattoir. Within the abattoir, infection from individual pigs contaminated the exterior of the carcass and pigs exposed to Salmonella in the lairage were infected. Salmonella can be introduced at various points in the pig production and slaughter process. Carcass contamination may arise from infection on farm and exposure in the lairage and abattoir environment. Pigs could be contaminated by previous batches of pigs while in lairage or during the dressing process. Salmonella infection on farms is dynamic with multiple serovars present from different sources. Molecular typing methods facilitated the tracing of Salm. Typhimurium through the production cycle and differentiated some farm-acquired from abattoir-acquired strains. The findings emphasize the importance of integrated control strategies along the pork food chain.
    Journal of Applied Microbiology 07/2011; 111(4):960-70. · 2.20 Impact Factor
  • R M Chalmers, R Smith, K Elwin, F A Clifton-Hadley, M Giles
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    ABSTRACT: In order to monitor epidemiological trends, Cryptosporidium-positive samples (n=4509) from diarrhoeic patients were typed. Compared to the previous 4 years, the proportion of Cryptosporidium hominis cases in 2004-2006 increased to 57·3%, while 38·5% were C. parvum. The remaining 4·2% cases included mixed C. parvum and C. hominis infections, C. meleagridis, C. felis, C. ubiquitum and a novel genotype. When the typing results were combined with enhanced surveillance data to monitor risk exposures, C. hominis was linked to urban dwelling, previous diarrhoea in the household, any travel especially abroad, and using a swimming or paddling pool. C. parvum was linked to having a private water supply, contact with surface water, visiting or living on a farm, and contact with farm animal faeces. The proportion of laboratory-confirmed indigenous cases acquired from direct contact with farm animals was estimated to be 25% for C. parvum and 10% of all reported Cryptosporidium cases.
    Epidemiology and Infection 05/2011; 139(5):700-12. · 2.87 Impact Factor
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    ABSTRACT: This is the first study comparing societal costs of acute illness with Salmonella Typhimurium (ST) and Salmonella Enteritidis (SE) in the UK. It included the cost and severity of the illness and explored the impact of each Salmonella serovar on the patients, their families, the NHS, and the wider economy. The study ascertained confirmed cases of ST and SE between July and November 2008. The mean costs per case were £1282 (ST) and £993 (SE). The indirect costs associated with the work-time lost by the case, parents, or carers were £409 (ST) and £228 (SE); this difference was statistically significant. The aggregate cost of ST and SE identified using laboratory test results for the UK as a whole was estimated as £6.5 million. Work-time lost and caring activities are cost categories that are not frequently investigated within the infectious intestinal disease literature, although they represent an important societal cost.
    Epidemiology and Infection 05/2011; 139(5):742-53. · 2.87 Impact Factor
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    ABSTRACT: to determine the prevalence of extended-spectrum β-lactamases (ESBLs) in Escherichia coli from poultry in Great Britain (GB). E. coli was isolated from 388 broiler chicken caecal samples from 22 abattoirs and from boot swabs from 442 turkey flocks over successive 1 year periods. CHROMagar ECC with and without cephalosporin antibiotics was used as isolation medium and the chicken study also used CHROMagar CTX. ESBL phenotype isolates were tested for the presence of bla(CTX-M,) bla(OXA), bla(SHV), bla(TEM) and ampC genes(.) CTX-M isolates were tested for O25 serogroup, replicon, CTX-M sequence, multilocus sequence type (MLST), PFGE type, plasmid transfer and qnrA, qnrB, qnrS, qepA and aac(6')-Ib genes. CTX-M-carrying E. coli were isolated from 54.5% of the broiler abattoirs and from 3.6% of individual broiler caecal samples and were CTX-M sequence types 1 (mainly), 3 and 15 with replicon types I1-γ, A/C and P/F, and I1-γ, respectively. CTX-M-carrying E. coli were isolated from 5.2% of turkey meat production farms and 6.9% of turkey breeder farms and were CTX-M sequence types 1, 14 (mainly), 15 and 55 with mainly replicon types F, FIA, K and I1-γ, respectively. None of the CTX-M isolates was serogroup O25. PFGE/MLST showed the CTX-M isolates to be clonally diverse, although MLST 156 with CTX-M-15 was isolated from both chickens and turkeys and has been previously reported in gulls. CTX-M-negative, ESBL- and bla(TEM)-positive strains were mainly TEM-52C. poultry-derived CTX-M E. coli in GB are different from major CTX-M sequence types causing disease in humans.
    Journal of Antimicrobial Chemotherapy 01/2011; 66(1):86-95. · 5.34 Impact Factor
  • J D Rodgers, F A Clifton-Hadley, C Marin, A B Vidal
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    ABSTRACT: To evaluate the culture specifications of the 2008 EU baseline survey for Campylobacter spp. in broiler flocks at slaughter, by assessing the detection of thermophilic Campylobacter in chicken caecal contents by culture on selective agar with or without enrichment culture. Additionally, to assess the impact of sample storage time on Campylobacter detection. Serial dilutions of pooled caeca samples in phosphate-buffered saline or Campylobacter-negative caecal contents were cultured micro-aerobically at 41.5°C on mCCDA, Karmali and Preston agars before and after enrichment in Exeter broth. Direct culture on mCCDA showed a higher isolation rate than for Karmali or Preston agars, but a similar isolation rate to enrichment. Enumeration of samples showed the numbers of viable bacteria dropped slightly during storage. Direct culture on mCCDA was the most sensitive method for detection of Campylobacter, and samples with 10(4) CFU g(-1) were still detectable after 6 days. Comparison of prevalence results from the 2008 EU baseline survey will need careful interpretation as the different media specified vary in their sensitivity to detect thermophilic Campylobacter. Delayed culture for up to 80 h after collection should have little impact on detection rate.
    Journal of Applied Microbiology 10/2010; 109(4):1244-52. · 2.20 Impact Factor
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    ABSTRACT: The study investigates farms suspected of being sources of zoonotic human cryptosporidiosis. A variety of implicated farm animal species were sampled and tested to detect Cryptosporidium oocysts and investigate genetic linkage with human patients. Risk factor information was collected from each farm and analysed by multivariable logistic regression to detect significant associations between factors and Cryptosporidium in animals. The results showed that average sample prevalence of Cryptosporidium infection was highest in cattle, sheep and pigs ( approximately 40-50%), in the mid-range in goats and horses (20-25%) and lowest in rabbits/guinea pigs, chickens and other birds ( approximately 4-7%). A single sample from a farm dog was also positive. Cryptosporidium parvum, which has zoonotic potential, was the commonest species and was most likely to be present in cattle and, to a lesser extent, in sheep. In particular, young calves and lambs shed C. parvum and this finding was corroborated in a statistical model which demonstrated that samples from groups of preweaned animals were 11 times, and immature animal groups six times, more likely to be positive than groups of adult animals, and that samples from a farm with a cattle enterprise were twice as likely to be positive than farms without a cattle enterprise. On seven out of eight farms, at least one C. parvum isolate from an animal sample was indistinguishable at the gp60 locus from those found in the human patients, indicating that farm animals are a likely source of infection for humans.
    Preventive Veterinary Medicine 04/2010; 94(1-2):9-17. · 2.39 Impact Factor
  • Luke Randall, Fabrizio Lemma, John Rodgers, Ana Vidal, Felicity Clifton-Hadley
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    ABSTRACT: A common problem of both conventional and real-time PCR assays is failure of DNA amplification due to the presence of inhibitory substances in samples. In view of this, our aim was to develop and evaluate internal amplification controls (IACs) for use with an existing duplex real-time PCR assay for Campylobacter coli and Campylobacter jejuni. Both competitive and non-competitive IACs were developed and evaluated. The competitive approach involved a DNA fragment of the coding region of the fish viral haemorrhagic septicaemia virus, flanked by the mapA PCR primers, whilst the non-competitive approach utilized an extra set of universal 16S rDNA primers. Both IAC-PCR assay types were evaluated using cultures of Campylobacter and chicken caecal content samples. Both IACs were sensitive to caecal inhibitors, making them suitable for detecting inhibition which could lead to false-negatives. Results showed that both IACs at optimum concentrations worked well without reducing the overall sensitivity of the PCR assay. Compared to culture, the optimized competitive IAC-PCR assay detected 45/47 positives (sensitivity 93.6 %, specificity 80.1 %); however, it had the advantage over culture in that it could detect mixed infections of C. coli and C. jejuni and was capable of giving a result for a sample within a day.
    Journal of Medical Microbiology 10/2009; 59(Pt 2):172-8. · 2.30 Impact Factor
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    ABSTRACT: Isolates of Salmonella enterica serovar Typhimurium belonging to definitive phage type (DT) 120 (Salmonella Typhimurium DT 120) from simultaneous outbreaks of infection in the England and Denmark have been compared on the basis of antibiogram, pulsed-field gel electrophoresis (PFGE), and multiple locus variable number tandem repeat analysis (MLVA). Isolates from England had the resistance profile (ampicillin, streptomycin, sulfamethoxazole, and tetracycline), MLVA profiles 2-4-4-0-2, 2-4-5-0-2, and 2-4-0-0-2, and the PFGE type STYMXB.0083. Representative isolates from the Denmark outbreak were resistant to ampicillin only (A) and had the MLVA type 2-12-6-0-2 and the PFGE type STYMXB.0010. These results demonstrated that outbreak isolates from England and Denmark were not identical. Subsequently, comparison of outbreak isolates with contemporary animal isolates showed that an isolate with the same PFGE type and a similar MLVA type had been isolated in England before its identification in Denmark. These results confirmed the usefulness of MLVA in international outbreak investigations of multiresistant Salmonella Typhimurium and have demonstrated how new molecular strategies may be used to supplement existing methods such as PFGE to enable the accurate and rapid comparison of isolates from different countries. The data also indicate that MLVA proves a useful method for detection of specific Salmonella Typhimurium DTs from human and veterinary sources.
    Microbial drug resistance (Larchmont, N.Y.) 06/2009; 15(2):133-8. · 1.99 Impact Factor
  • R P Smith, J Ellis-Iversen, E L Snary, F A Clifton-Hadley, G A Paiba
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    ABSTRACT: To investigate the factors influencing the presence and burden of Escherichia coli O157 in farm wastes. Wastes from six cattle farms were screened for the presence and concentration of E. coli O157 and E. coli on three occasions over a year and waste management data were collected. Sixty-three of 878 (7.1%) samples were positive for verocytotoxigenic Escherichia coli O157 and 664/875 (75.9%) for E. coli with detectable levels greater in fresh waste than in stored waste, pasture or dirty water. The turning/stirring of stored waste and the use of more than one store (allowing longer storage times) reduced the proportion of E. coli O157 positive samples. The presence of E. coli O157 significantly reduced from a high prevalence found in fresh faeces and stored waste to lower proportions in dirty water and pasture samples. Escherichia coli O157 was only detected on pasture when waste was spread from contaminated stores the day before sampling. A high prevalence of positive E. coli O157 samples were detected when cattle were re-housed. These findings help to support the importance of treating and storing farm waste, as well as providing evidence for the level of dilution of E. coli O157 from fresh waste to recently spread pastures.
    Journal of Applied Microbiology 03/2009; 106(2):613-23. · 2.20 Impact Factor
  • The Veterinary record 02/2009; 164(1):24-5. · 1.80 Impact Factor
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    ABSTRACT: A 12-month abattoir study was undertaken from January 2003. We collected 7492 intestinal samples from cattle, sheep and pigs at slaughter. Rectal samples were taken from cattle and sheep and caecal samples from pigs. They were examined for verocytotoxigenic E. coli (VTEC) O157, Salmonella, thermophilic Campylobacter and Yersinia enterocolitica. Data were collected on the animal from which the sample came and this information was analysed to look at potential risk factors for carriage of these organisms. Logistic regression models were run where an adequate number of positive results were available. This revealed that VTEC O157 carriage in cattle was associated with the summer period and that age was a protective factor. Salmonella carriage in pigs was associated with lairage times >12 h, the North East and not feeding when there was no bedding available. In cattle, carriage was associated with the summer period, the Eastern region of GB and dairy animals. In sheep a spring seasonal effect was seen, which coincided with the lambing period. The carriage of thermophilic Campylobacter in cattle was associated with single-species abattoirs, with age a protective factor. In sheep, winter was a risk period with lairage management influential. For pigs, lairage times of <12 h were found to be associated with carriage. A seasonal trend for carriage of Y. enterocolitica in all species was demonstrated with the period December-May a risk. For cattle, age was also a risk factor; for sheep feeding in the lairage and for pigs being held overnight were risk factors.
    Epidemiology and Infection 02/2009; 137(8):1135-48. · 2.87 Impact Factor

Publication Stats

668 Citations
141.48 Total Impact Points

Institutions

  • 2011
    • Nottinghamshire Healthcare NHS Trust
      Nottigham, England, United Kingdom
  • 2010
    • WWF United Kingdom
      Londinium, England, United Kingdom
  • 2008–2009
    • University of Reading
      • School of Agriculture, Policy and Development
      Reading, ENG, United Kingdom
  • 2001
    • University of Bristol
      • School of Veterinary Sciences
      Bristol, ENG, United Kingdom