UK-wide risk factor study of broiler carcases highly contaminated with Campylobacter

Campylobacter is a major cause of food poisoning and is typically the most common cause of gastroenteritis in the UK. Data collected at broiler farm and abattoir level, for slaughter batches that were sampled for UK-wide monitoring, were used to generate two epidemiological risk factor models. A total of 483 batches slaughtered between January 2016 and March 2017 were used in the analysis, coming from 19 abattoirs representing more than 85% of UK broiler production. For each selected slaughter batch, one carcase was sampled after primary chilling and 10 randomly sampled birds had caecal samples collected at the evisceration point. Samples were used for Campylobacter identification and quantification. Two multivariable mixed-effects models were designed, one with the binary outcome for the detection of a highly contaminated (>1000 colony forming units (CFU)/g) Campylobacter-positive carcase, whereas the other used the Campylobacter colony count (CFU/g) carcase outcome. The results suggest that caecal colonization within the batch was a key factor for the occurrence of Campylobacter on carcases, and many factors that were identified in the model were also likely to be related to colonization or related to the risk of introduction of Campylobacter from partial depopulation (referred to as thinning) of ~30% of the flock approximately 1 week before full flock depopulation events. The amount of neck skin in the sample was another key factor identified and was included in both models as a risk factor. The models have also identified other factors which may be related to the general health and husbandry on-farm (use of prebiotics or vaccines, and identification of the product used for drinking line cleaning), whereas the other factors may identify control points related to transmission within a farm. The identification of these variables could help focus control efforts on-farm, especially for relatively easy improvements, such as improving the provision of house-specific bird-weighing buckets/cages in houses.

Study of Salmonella detection in laying hens using a Bayesian model

As part of the measures to reduce the prevalence of Salmonella in poultry in the UK, National Control Programmes (NCPs) have been implemented. These involve regular statutory testing of poultry holdings to monitor and estimate the prevalence of Salmonella in the national flock population and to control Salmonella on holdings with positive flocks, especially those serovars most identified with human illness: Salmonella Enteritidis (SE) and S. Typhimurium (ST). It is very important to ensure that the level of testing is appropriate so that it is sufficiently effective to identify positive flocks and to monitor prevalence, but also efficient in the use of resources. The aim of this study was to estimate the sensitivity of both the Operator and Competent Authority (CA) Official sampling used to detect infected flocks, and to also estimate the true proportion of infected holdings of commercial laying flocks in GB each year of the NCP, along with the trend of any changes in prevalence for both SE/ST and non-SE/ST. A Bayesian model was developed to estimate the sensitivity of both Operator and CA Official sampling from the NCP data 2009-2018, and to estimate the true prevalence of infected holdings. The model estimate for the prevalence of infected holdings for the first complete year of the NCP was 3.9% (95% Credible Interval (CI) 2.8-6.2%) for non-SE/ST and 0.8% (95% CI: 0.4%-1.5%) for SE/ST. Prevalence had reduced to 1.6% (non-SE/ST) (95% CI 1.0%-2.5%) and 0.2% (SE/ST) (95% CI 0.1%-0.4%) in 2018. Results indicated a very low sensitivity of Operator sampling (~9%), but a much higher sensitivity of CA Official sampling (~44%). The true prevalence of Salmonella infected holdings in the UK had a mean average reduction of 10.6% (95% CI: 6.3%-15.1%) per annum (non-SE/ST) and 15.9% (95% CI: 6.0%-19.8%) annual reduction for SE/ST. This has shown the effectiveness of the NCP for Salmonella in commercial laying flocks, with reductions in Salmonella overall more or less equal to the target reduction for regulated serovars of 10% per annum. The true prevalence of SE/ST was estimated to be below the final target of less than 2% in every year and was below 0.5% at the end of the 10 year period.

Convolutional neural network transformer (CNNT) for free-breathing real-time cine imaging

Funding Acknowledgements

Type of funding sources: None.

Background

Real-time cine imaging does not require breath-holding and is a robust cine imaging technique in the presence of irregular heartbeats. It is a good alternative to the conventional breath-hold retro-gated cine for simplified acquisition and improved patient comfort. Real-time acquisition is achieved with the single-shot BSSFP readout without retro-gating. To maintain good temporal and spatial resolution, higher acceleration (e.g. >4x parallel imaging) is required. As a result, the real-time cine images experience reduced signal-to-noise ratio (SNR), which limits its clinical acceptance.

Purpose

We developed a novel deep learning model architecture, the Convolutional Neural Network Transformer (CNNT), to improve the quality of real-time cine, under 4x, 5x and 6x acceleration.

Method

Convolutional Neural Networks (CNN) are widely used in CMR research to process cardiac images. Cardiac images are often acquired as a time series with strong inter-phase correlation. We combined the CNN with the more recent transformer model to develop a novel CNNT architecture. It takes in the entire 2D+T time series as input and has advantages of CNN for efficient computation and spatial invariance. It further inherits the advantages of attention layer in the transformer and is able to efficiently utilize the temporal correlation within a time series.

A CNNT model is developed to improve the SNR of real-time cine imaging. N=10 patients were scanned at a heart center, with 4x, 5x and 6x acceleration. Typical imaging parameters are: FOV 360×270mm2, flip angle 50°, acquired matrix size 160×90 for R=4 acceleration, 192×108 for R=5 and 6, temporal resolution 40ms for R=4, 42ms for R=5 and 35ms for R=6. The real-time images went through a TGRAPPA reconstruction [1] and the CNNT model. The SNR of TGRAPPA was measured with SNR units [2]. The Monte-Carlo pseudo-replica test was used to measure SNR for the CNNT model. For every cine series, two phases were picked for the end-systole and end-diastole. For every image picked, two region-of-interests were drawn in the myocardium and in the LV blood pool. The CNNT model was deployed inline on the MR scanner using the Gadgetron InlineAI [3].

Results

Figure 1 gives real-time cine images for three accelerations, reconstructed with TGRAPPA and CNNT. The parallel imaging TGRAPPA reconstruction suffers significant SNR loss from elevated g-factor and less acquired data. The deep learning CNNT model recovered SNR even at the very high 6x acceleration, without observed loss of boundary sharpness.

Table 1 lists the SNR measurement results. The TGRAPPA SNR decreased ∼4x from R=4 to R=6 for both the blood and myocardium. For the blood, the CNNT increased the SNR by 170%, 335%, 371% at R=4, 5 and 6. For the myocardium, the SNR increases were 335%, 634% and 828%.

Conclusion

We developed a convolutional neural network transformer model to recover the SNR for real-time cine imaging at higher acceleration.

Asymmetric septal thickening is observed in hypertrophic cardiomyopathy mutation carriers without left ventricular hypertrophy: insights from AI analysis

Funding Acknowledgements

Type of funding sources: Private grant(s) and/or Sponsorship. Main funding source(s): Dr Hughes is supported by the British Heart Foundation (grant number FS/17/82/33222).

Background

Hypertrophic cardiomyopathy (HCM) is a common inherited cardiac disease characterised by left ventricular hypertrophy (LVH), often, with asymmetric septal thickening. Despite the prevalence of inherited mutations present in >50% of cases, there is variable phenotypic expression in those with abnormal sarcomere protein genes. In individuals with abnormal genes but without LVH, we hypothesised that there is subtle asymmetric septal hypertrophy, detectable by the increased precision offered by an artificial intelligence (AI) tool for measuring wall thickness.

Purpose

We explored the septal-lateral ratio measured by AI in individuals with an identified genotype but no left ventricular hypertrophy as a component of sub-clinical HCM.

Methods

43 individuals with identified genotype, but no left ventricular hypertrophy (G+LVH-) and 97 age-, sex- and disease-matched controls underwent CMR. Patients were excluded if they had a maximum wall thickness (MWT) of ≥13mm. A clinically validated AI tool was used to measure the MWT, for each segment in the 16-segment AHA model. The septal-lateral ratio was calculated using the septal segment with the largest MWT and the lateral segment with the largest MWT.

Results

The mean septal-lateral ratio of the G+LVH- patients was 1.22 (SD 0.22) and the mean septal-lateral ratio of the matched controls was 1.14 (SD 0.15) with a statistically significant mean difference of 0.08 (p=0.01). There was no significant difference between the MWT of the G+LVH- patients at 10.3mm (SD 2.2) and healthy volunteers at 10.1mm (SD 1.8) (p = 0.61).

Conclusion

G+LVH- patients have a 7% increase in their septal-lateral ratio compared with age-matched controls despite the lack of difference in the MWT. Using increased precision offered by AI, early features of HCM can be observed in patients without overt LVH.

CNNT DB-LGE: free-breathing dark blood late enhancement imaging using the convolutional neural network transformer speeds acquisition by 50%

Funding Acknowledgements

Type of funding sources: Public grant(s) – National budget only. Main funding source(s): Supported in part by the Division of Intramural Research of the National Heart, Lung, and Blood Institute, National Institutes of Health (grants Z1A-HL006214-05 and Z1A-HL006242-02).

Background

Dark blood late gadolinium enhancement (DB-LGE) imaging shows superior delineation of myocardial infarction (MI), especially at the sub-endocardial boundary. Our previous study [1] developed a free-breathing DB-LGE with the single shot SSFP readout, phase sensitive inversion recovery (PSIR) reconstruction, and respiratory motion corrected averaging. To compensate the potential signal-to-noise ratio loss, our previous DB-LGE doubled the measurements, thereby increasing the acquisition time.

Purpose

In this study, we developed a deep learning image enhancement model using a novel neural network architecture called the convolutional neural network transformer (CNNT) to improve the image quality of DB-LGE and to reduce the acquisition time by decreasing the number of measurements.

Methods

A novel image enhancement model was developed using a novel network architecture called the Convolutional Neural Network Transformer (CNNT) proposed by us. This architecture is suitable for the 2D+Time CMR acquisition, by exploiting the temporal correlation between images over multiple averages.

The evaluation was first retrospectively conducted on a cohort of 12 patients acquired with the original protocol [1] using the full 16 measurements. For every subject, a complete short-axis stack (typically 12 slices) was acquired to cover the entire left ventricular. The imaging data was reconstructed in three ways. Original: using all acquired 16 measurements. This is our base-line protocol. Original 50%: using only the first 8 measurements. CNNT 50%: using only the first 8 averages, but performing the CNNT deep learning image enhancement before MOCO PSIR reconstruction. Two experienced imaging researchers (PK and MF, >10 years of experience for both) scored all DB-LGE images for the overall quality, diagnostic confidence and delineation of MI/boundaries (5 = excellent, 4 = good, 3 = fair, 2 = poor, and 1 = non-diagnostic). The CNNT DB-LGE was deployed to the MR scanner using the Gadgetron InlineAI [2].

Results

Figure 1 gives examples of DB-LGE with three reconstruction methods. The CNNT image has higher SNR and well delineated MI. The Original images with the longest acquisition have good quality and the Original-50% acquired with 8 measurements are good quality but have reduced SNR. The mean scores for overall image quality, diagnostic confidence and MI delineation of two reviewers were 4.88±0.23, 4.88±0.23, 4.83±0.25 for CNNT and 4.96±0.14, 4.96±0.14, 4.67±0.39 for the original approach. No significant differences were found between the original and the CNNT (P>0.15 for all).

Figure 2 shows an acute MI patient prospectively acquired with the 50% scan time reduction, with and without the CNNT enhancement. The resulting PSIR images well delineate the MVO due to the acute MI, with improved SNR.

Conclusion

A novel CNNT model was proposed and evaluated to speed up the free-breathing MOCO DB LGE by 50% without sacrificing image quality.

Improving the diagnostic accuracy of apical hypertrophic cardiomyopathy using machine learning

Funding Acknowledgements

Type of funding sources: Private grant(s) and/or Sponsorship. Main funding source(s): Dr Hughes is supported by the British Heart Foundation (grant number FS/17/82/33222).

Introduction

The imaging criteria for diagnosis of apical hypertrophic cardiomyopathy (ApHCM) is a maximum wall thickness (MWT) ≥15mm. CMR enables detection of subtle phenotypic features (e.g. loss of apical tapering, cavity obliteration) and coupled with characteristic electrocardiogram changes, ApHCM can be diagnosed without overt hypertrophy. However, these patients are not captured by current diagnostic criteria.

Purpose

We sought to use a machine learning tool to quantify wall thickness and identify patients with ‘relative’ ApHCM that do not reach current diagnostic thresholds.

Methods

CMR images from 4118 healthy participants from the UK Biobank were segmented automatically with a clinically validated machine learning algorithm and wall thickness measured at all point in the myocardium by solving a solution to Laplace’s equation. MWT were pooled into 16 AHA segments and indexed to body surface area (BSA). The non-indexed and indexed segmental upper limit of normal was calculated as the mean + 3 standard deviations (the equivalent of 95% confidence interval after correcting for multiple [16] comparisons using the Bonferroni method).

Results

73 overt ApHCM subjects (MWT>15mm) and 31 relative ApHCM subjects underwent CMR scanning. In healthy controls, the non-indexed (and indexed) upper limits were calculated for the apical-anterior 10.2mm (5.2 mm/m2), apical-septal 11.1mm (5.6 mm/m2), apical-inferior 10.5mm (5.3 mm/m2) and apical-lateral 10.1mm (5.2 mm/m2) segments. With a non-indexed cut-off, all (73 of 73) overt ApHCM and 84% (26 of 31) relative ApHCM were classified as having an abnormally thick apex. 3% (127 of 4118) of the healthy UK Biobank cohort were classified as abnormal, as expected. Using an indexed cut-off, all overt ApHCM and 87% (27/31) relative ApHCM were classified as abnormal, and 3% (123 of 4118) of the healthy UK Biobank cohort were misclassified.

Conclusion

We can successfully classify 87% of relative ApHCM patients from a normative reference range derived from a large cohort of healthy patients – a significant improvement on existing methods. We show that the specificity and sensitivity is increased when MWT is indexed to BSA. For practical clinical application, we recommend a cut-off of 10mm or an indexed cut-off of 5mm/m2 in any apical segment to diagnose apical LVH. Overt and relative apical HCM examplesHealthy controls AHA maps (non-indexed)

Speeding up cardiac MR segmentation with semi-supervision: applications in cine imaging

Funding Acknowledgements

Type of funding sources: Private company. Main funding source(s): This material is based upon work supported by the Google Cloud Research Credits program with the award GCP19980904.

Background

Segmentation is an important postprocessing step in cardiac magnetic resonance (CMR) imaging that enables quantitative assessment of functional parameters. Deep learning can automate the segmentation process, producing accurate contours of cardiac structures while reducing the time required to analyze images and the interobserver variation compared to manual analysis. However, common approaches to training neural networks (NNs) require large amounts of labeled data, which is costly to generate and slows down the development of CMR segmentation NNs for new applications. Semi-supervision is an approach to alleviate this labeling burden by relying on abundant unlabeled data and a smaller amount of labeled data to train NNs.

Purpose

We propose a novel semi-supervised method to train CMR segmentation NNs. We use the proposed method to train NNs to segment the left ventricle in CMR cine images. Ultimately, we aim to show that semi-supervision can drastically reduce the amount of labeled data required to develop machine learning segmentation applications for CMR while maintaining high performance.

Methods

Our dataset consists of 1,208 short-axis cine CMR images and 1,244 long-axis cine CMR images. An expert annotator manually segmented the endocardium on the end-diastolic and end-systolic short-axis and long-axis images and the epicardium on the end-diastolic short-axis images. We split the dataset randomly by patient into 60% training, 20% validation, and 20% testing data. We train semi-supervised segmentation networks using a supervised cross-entropy loss to learn from the labeled training data and a cosine embedding loss in addition to a pseudo-labeling step to learn from the unlabeled training data. To evaluate how performance changes with different amounts of labeled training data, we vary the percent of training data that has labels from <1%-100%. We evaluate the predicted segmentation masks using the Dice coefficient.

Results

Using only 100 labeled image slices, the semi-supervised segmentation NNs achieve a mean Dice coefficient within 1.10% of networks trained with fully labeled training sets, corresponding to >85% reduction in required labeled training data (Table 1). The proposed semi-supervised method improves performance over naïve training by 6.21% for the most limited labeled data setting (i.e., 10 labeled image slices; Figure 1).

Conclusion

We have shown that NNs trained with limited labeled data achieve high performance on left ventricle segmentation in short-axis and long-axis CMR cines. The proposed approach is flexible and broadly applicable to different CMR segmentation tasks, enabling rapid development of segmentation networks for many cardiac structures and applications. Table 1Figure 1

Observations on the distribution and control of Salmonella in commercial broiler hatcheries in Great Britain

Salmonella can enter hatcheries via contaminated eggs and other breaches of biosecurity. The study examined the prevalence and distribution of Salmonella in commercial hatcheries and assessed the effects of providing advice on Salmonella control. Intensive swab sampling was performed throughout 23 broiler hatcheries in Great Britain (GB). Swabs were cultured using a modified ISO6579:2017 method. After each visit, tailored advice on biosecurity and cleaning and disinfection procedures was provided to the hatchery managers. Repeat sampling was carried out in 10 of the 23 hatcheries. Salmonella prevalence ranged between 0% and 33.5%, with the chick handling areas, hatcher areas, macerator area, tray wash/storage areas, external areas and other waste handling areas being more contaminated than the setter areas. Salmonella Senftenberg and Salmonella 13,23:i:‐ were the most commonly isolated serovars. There was a reduction in Salmonella prevalence at the second visit in eight out of 10 premises, but prevalence values had increased again in all of the improved hatcheries that were visited a third time. One hatchery harboured a difficult‐to‐control resident Salmonella 13,23:i:‐ strain and was visited six times; by the final visit, Salmonella prevalence was 2.3%, reduced from a high of 23.1%. In conclusion, the study found low‐level Salmonella contamination in some GB broiler hatcheries, with certain hatcheries being more severely affected. Furthermore, it was shown that Salmonella typically is difficult to eradicate from contaminated hatcheries, but substantial reductions in prevalence are possible with improvements to biosecurity, cleaning and disinfection.

Risk factor analysis for Salmonella contamination of broiler chicken (Gallus gallus) hatcheries in Great Britain

Salmonellosis is the second most commonly reported zoonosis in the European Union and contaminated meat from broiler chickens (Gallus gallus) is an important source of human infection. In Great Britain (GB), prevalence of Salmonella enterica in broiler flocks is low, having declined considerably since the introduction of the Salmonella National Control Programme in 2010. However, this decreasing trend has stabilised in recent years and serovars with known ability to persistently colonise hatcheries have been isolated from broiler flocks with increasing frequency, indicating that further controls on hatchery contamination are required. The broiler industry in GB has changed dramatically over the last 15 years, with greater intensification and dominance by a small number of very large companies which rely on relatively few hatcheries. An investigation of risk factors for Salmonella contamination in GB broiler hatcheries was therefore carried out so that relevant up-to-date advice on Salmonella control can be provided. Twenty-two hatcheries, representing most commercial scale GB broiler hatcheries, were visited between 2015 and 2018. Salmonella contamination was comprehensively investigated at each hatchery by collecting between 108 and 421 environmental swab samples per hatchery (6990 samples in total from all hatcheries). An in-depth questionnaire on hatchery operations was completed for each hatchery, and results were incorporated into a risk factor analysis (univariable followed by multivariable mixed effects logistic regression) to identify factors associated with Salmonella occurrence. Overall, 6.0 % (416/6990) of environmental samples were Salmonella-positive and Salmonella was isolated from 17/22 hatcheries. Ten different serovars were isolated, the most common being S. Senftenberg and S. Mbandaka which are known hatchery colonisers. Sixty-four risk factor variables were investigated. Twenty-two of these were initially retained based on univariable analyses (p ≤ 0.25) and six were ultimately left in the final multivariable model (p ≤ 0.05). Salmonella detection was positively associated with having ≥30 hatchers in regular use compared to fewer (Odds ratio [OR] 23.7, 95 % confidence interval [CI] 6.7-84.2), storing trays in process rooms (OR 28.8, CI 7.8-106.3), drying set-up trolleys in corridors (OR 15.6, CI 5.9-41.4) and having skips located in enclosed areas (OR 8.99, CI 5.89-41.35). Using a closed waste disposal system was negatively associated with Salmonella detection (OR 0.08, CI 0.04-0.18) and the odds of detecting Salmonella in hatcheries with 31-60 total workers was lower compared to hatcheries with ≤30 staff (OR 0.16, CI 0.06-0.40). Despite the complexities of hatchery enterprises, changes to a relatively small number of features may significantly reduce the occurrence of hatchery contamination.

Disinfection to control African swine fever virus: a UK perspective

A review of African swine fever (ASF) was conducted, including manifestations of disease, its transmission and environmental persistence of ASF virus. Findings on infectious doses of contemporary highly-pathogenic strains isolated from outbreaks in Eastern Europe were included. Published data on disinfectant susceptibility of ASF virus were then compared with similar findings for selected other infectious agents, principally those used in the UK disinfectant approvals tests relating to relevant Disease Orders for the control of notifiable and zoonotic diseases of livestock. These are: swine vesicular disease virus, foot and mouth disease virus, Newcastle disease virus and Salmonella enterica serovar Enteritidis. The comparative data thus obtained, presented in a series of charts, facilitated estimates of efficacy against ASF virus for some UK approved disinfectants when applied at their respective General Orders concentrations. Substantial data gaps were encountered for several disinfectant agents or classes, including peracetic acid, quaternary ammonium compounds and products based on phenols and cresols.

Disinfectant testing for veterinary and agricultural applications: A review

Disinfectants for veterinary and livestock use, plus skin antiseptics, are critical elements for the control of infectious agents, including zoonotic and antimicrobial-resistant micro-organisms, in managed animal species. Such agents impact animal welfare, economic performance and human health. Testing of disinfectants is needed for safety, efficacy and quality control. The present review examines the principal types of test (carrier, suspension, surface and field) that have been developed or attempted, plus the features inherent in the respective tests, particularly with respect to variability. Elements of testing that have to be controlled, or which can be manipulated, are discussed in the context of real-world scenarios and anticipated applications. Current national and international testing regimes are considered, with an emphasis on the UK, continental Europe and North America, and with further detail provided in the Supporting Information. Challenges to disinfectant efficacy include: the nature of the biological targets (bacteria, fungi, yeasts, spores, viruses and prions), the need for economical and safe working concentrations, the physical and chemical nature of contaminated surfaces, constraints on contact times and temperatures, the presence of organic soil and other barrier or neutralising substances (including biofilms), and thoroughness of pre-cleaning and disinfectant application. The principal challenges with veterinary disinfectant testing are the control of test variability, and relating test results to likely performance in variable field conditions. Despite some ambitions to develop standardised field tests for disinfectants, aside from skin antiseptic trials the myriad problems such tests pose with respect to cost, reproducibility and generalisability remain intractable.

Interaction of stroke volume and myocardial phenotype in patients with severe aortic stenosis referred for intervention: outcome data from the BSCMR AS700 study

Funding Acknowledgements

Type of funding sources: None.

onbehalf

The BSCMR Valve Consortium

Background

 Patients with low-flow aortic stenosis (LF-AS) have higher mortality than those with high-flow severe AS.  The conventional echocardiographic definition of LF-AS is an indexed stroke volume (SVi) <35ml/m2. Whether this cut-off translates to cardiac magnetic resonance (CMR), and how CMR SVi associates with myocardial remodelling (volume/function/scar) and survival is unclear.

Purpose

 To determine the association between CMR SVi, myocardial remodelling and survival in severe symptomatic AS. 

Methods

  In a multi-centre longitudinal outcome study of patients with severe AS listed for either surgical (SAVR) or transcatheter aortic valve intervention (TAVI) at six cardiothoracic centres, survival was assessed and stratified by SVi. Patients underwent preprocedural echocardiography and CMR between January 2003 and May 2015.  Standardised core-lab analyses on pre-procedural CMR for biventricular volumes, function and scar quantification were performed. All-cause and cardiovascular mortality were tracked for a minimum of two years after AVR.

Results

 A total of 674 patients with severe AS (age 75 ± 14years; 63% male, aortic valve area 0.4 ± 0.1 cm2/m2) were included.  Patients with low SVi by CMR <35ml/m2 were older and had a greater burden of comorbidities (atrial fibrillation [AF], diabetes, high BMI). Independent predictors of SVi were age, AF, increased left atrial volume, aortic valve regurgitant fraction and left ventricular mass (LV) mass index (by CMR). There was no difference in SVi with choice of intervention (TAVI vs SAVR) or presence of late gadolinium enhancement. In multivariate analysis (Table 1), SVi was associated with cardiovascular mortality in the whole cohort (HR 0.97, 95%CI 0.95-0.99, p = 0.02), and all-cause mortality after TAVI (HR 0.97, 95%CI 0.95-0.99, p = 0.006) but not SAVR (p = 0.6). Adjusted mortality hazard increases below 50ml/m2 and plateaus between 35-40ml/m2 (Figure 1A), adjusted for LGE, STS score (Society of Thoracic Surgery score) and wall thickness.

Conclusion

SVi by CMR is an independent predictor of cardiovascular mortality. Mortality hazard increases progressively below a SVi of 50mL/m2.

Abstract Figure 1

Trends in Salmonella serovars and antimicrobial resistance in pigs and poultry in Northern Ireland between 1997 and 2016

BACKGROUND

In the EU, salmonellosis is the second most commonly reported zoonosis. This pattern is reflected in Northern Ireland. Historically, foodborne salmonellosis has largely been attributed to the consumption of poultry products, and as such a number of legislative measures have been introduced by the EC. These policies focus mainly on five target Salmonella serovars.

METHODS

Here the authors present a descriptive analysis of 20 years of data from the Northern Ireland National Reference Laboratory for Salmonella.

RESULTS

The study's results show, for poultry submissions, a large decrease in the detection of four of the five targeted Salmonella serovars over the study period, with the fifth serovar undetected throughout the study. Additionally, there was an increase in the detection of a number of other non-regulated serovars. In pigs, S Typhimurium, which is among the most common causes of human salmonellosis, was the most commonly isolated serovar. When comparing levels of antimicrobial resistance in S Typhimurium between livestock groups, the authors found a decrease over time in poultry, but an increase in pigs, highlighting the potential significance of pigs in addressing public health concerns.

CONCLUSION

The authors conclude that continued surveillance is important in the assessment of control measures at a national and transnational scale.

Abstract P6-17-13: ZW49, a HER2 targeted biparatopic antibody drug conjugate for the treatment of HER2 expressing cancers

Background: HER2-targeted therapies have transformed the treatment of patients with HER2-expressing breast and gastric cancers. Despite this, there remains a need for new treatments that are well tolerated and effective not only for cancers with high HER2 expression levels but also those with lower levels of expression. ZW49 is an antibody drug conjugate (ADC) that combines a novel auristatin payload (potent anti-cancer agent) with the unique mechanisms of action of the anti-HER2 biparatopic antibody, ZW25, which binds to the same domains as trastuzumab and pertuzumab. In preclinical studies in cancer cell lines with low to high levels of HER2 expression, ZW25 is associated with increased binding and internalization compared to trastuzumab, while the novel N-acyl sulfonamide auristatin payload has demonstrated increased in vivo tolerability compared to other microtubule inhibitors. ZW49 therefore has the potential to address unmet medical need across a range of HER2-expressing cancers.

Methods: Multiple in vitro and in vivo experiments were performed to characterize ZW49 as a potential therapeutic candidate. Internalization and cell growth inhibition of ZW49 were evaluated in HER2-expressing cell lines. Anti-tumor activity was assessed in patient-derived xenograft (PDX) tumor models of HER2 low and high expressing breast cancers. Tolerability was assessed in a 6-week repeat-dose non-GLP toxicology study in non-human primates (NHP) with intravenous administration of ZW49 at either 9 mg/kg or 12 mg/kg once every two weeks.

Results: In vitro, ZW49 was more rapidly internalized into HER2-expressing cells compared to a monospecific trastuzumab-ADC. ZW49 also displayed potent in vitro cell growth inhibition in several breast cancer cell lines with a range of HER2 expression. This activity was confirmed in multiple in vivo PDX models, including a HER2 IHC 3+ HBCx-13b xenograft where two doses of ZW49 at 3 mg/kg or higher generated tumor regressions, and a HER2 IHC 1+ ST-910 xenograft where a single dose of ZW49 at 6 mg/kg or higher generated regressions. In both models, regressions occurred at exposures that were well tolerated in NHP. In a repeat dose pilot non-GLP study the highest dose tested (12 mg/kg) was considered to be the no observed adverse effect level (NOAEL) and a GLP repeat-dose toxicology study was ongoing at the time of abstract submission.

Conclusions: ZW49 is a novel biparatopic HER2-targeted ADC that demonstrated anti-tumor activity in low and high HER2-expressing breast cancer cell lines and PDX models. Notably, tumor regressions were observed at exposure levels that were well tolerated in NHP. These results support the potential of ZW49 as a novel therapeutic agent that may help address unmet medical need in patients with high and low HER2-expressing cancers.

Citation Format: Hamblett KJ, Barnscher SD, Davies RH, Hammond PW, Hernandez A, Wickman GR, Fung VK, Ding T, Garnett G, Galey AS, Zwierzchowski P, Clavette BC, Winters GC, Rich JR, Rowse GJ, Babcook JS, Hausman D. ZW49, a HER2 targeted biparatopic antibody drug conjugate for the treatment of HER2 expressing cancers [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P6-17-13.

Field Interventions Against Colonization of Broilers by Campylobacter

Poultry accounts for a high proportion of human campylobacteriosis cases, and the problem of Campylobacter colonization of broiler flocks has proven to be intractable. Owing to their broad host range and genetic instability, Campylobacter organisms are ubiquitous and adaptable in the broiler farm environment, colonizing birds heavily and spreading rapidly after introduction into a flock. This review examines strategies to prevent or suppress such colonization, with a heavy emphasis on field investigations. Attempts to exclude Campylobacter via enhanced biosecurity and hygiene measures have met with mixed success. Reasons for this are becoming better understood as investigations focus on houses, ventilation, biosecurity practices, external operators, and compliance, among other factors. It is evident that piecemeal approaches are likely to fail. Complementary measures include feed and drinking water treatments applied in either preventive or suppressive modes using agents including organic acids and their derivatives, also litter treatments, probiotics, prebiotics, and alterations to diet. Some treatments aim to reduce the number of Campylobacter organisms entering abattoirs by suppressing intestinal colonization just before slaughter; these include acid water treatment or administration of bacteriophages or bacteriocins. Experimental vaccines historically have had little success, but some recent subunit vaccines show promise. Overall, there is wide variation in the control achieved, and consistency and harmonization of trials is needed to enable robust evaluation. There is also some potential to breed for resistance to Campylobacter. Good and consistent control of flock colonization by Campylobacter may require an as-yet undetermined combination of excellent biosecurity plus complementary measures.

Observations on the distribution and persistence of monophasic Salmonella Typhimurium on infected pig and cattle farms

Following a rapid rise in cases of monophasic Salmonella Typhimurium DT193 (mST) in humans and pigs since 2007 a detailed study of the prevalence and persistence of mST on pig and cattle farms in Great Britain (GB) was undertaken. Thirteen commercial pig farms and twelve cattle farms, identified as mST-positive from surveillance data, were intensively sampled over a three year period. Five indoor and eight outdoor pig farms and four beef and eight dairy farms were included. Individual and pooled faecal samples were collected from each epidemiological group and environmental samples throughout each farm and the antimicrobial resistance profile determined for a selection of mST-positive isolates. Indoor pig farms had a higher mST prevalence than outdoor pig farms, and across both cattle and pig farms the juvenile animals had a higher mST prevalence than the adult animals. Overall, mST prevalence decreased with time across all pig farms, from 25% to less than 15% of environmental samples and 22% to 15% of pooled faecal samples; only one organic outdoor breeding farm was Salmonella-negative at the end of the study. Across the cattle farms no mST was detected by the end of the study, apart from one persistent farm. Clearance time of mST was between seven and twenty-five months. Farms were selected based on having the antimicrobial resistance profile ampicillin, streptomycin, sulphonamides and tetracycline (A, S, SU, T), although resistance to trimethoprim-potentiated sulphamethoxazole was also identified on five pig farms sampled. This study provided a detailed insight into the distribution and persistence of mST on individual pig and cattle farms in GB. It has identified variation in mST shedding of individual animals, and the data can be applied to the wider livestock industry when considering the distribution of mST once identified on an individual farm.

Small animal disease surveillance: GI disease and salmonellosis

Presentation for gastrointestinal (GI) disease comprised 2.2 per cent of cat, 3.2 per cent of dog and 2.2 per cent of rabbit consultations between April 1, 2016 and March 31, 2017Diarrhoea and vomiting without blood were the most frequently reported GI disease clinical signs (34.4 and 38.9 per cent in cats and 42.8 and 37.3 per cent in dogs, respectively)The mean percentage of samples testing positive for Salmonella in dogs was double that in cats (0.82 per cent and 0.41 per cent, respectively) from January 1, 2011 to December 31, 2016In dogs, autumn was associated with a greater proportion of Salmonella-positive sample submissions; no clear suggestion of seasonal variation in cats was observedIn both cats and dogs, isolates belonging to Salmonella enterica group B serotypes were the most common (68.9 per cent in cats and 55.0 per cent in dogs).

Evaluation of an enhanced cleaning and disinfection protocol in Salmonella contaminated pig holdings in the United Kingdom

Salmonella is the second most commonly reported zoonotic gastrointestinal pathogen in the European Union, and a significant proportion of the cases are linked to the consumption of contaminated pork. Reduction of Salmonella at the farm level helps to mininimise the contamination pressure at the slaughterhouse, and therefore the number of Salmonella bacteria entering the food chain. Cleaning and disinfection (C&D) between batches of pigs is an intervention measure that has potential to reduce the transmission of Salmonella contamination within farms. In this study, two pig finisher buildings in each of 10 Salmonella positive farms were sampled pre-C&D, post-C&D, post-restocking with the following batch of pigs, and shortly before these pigs were sent to slaughter. The incoming batch of pigs was also sampled before it reached the study building (pre-restocking). At each visit, pooled and individual faecal samples were collected and Salmonella isolation was carried out according to an ISO 6579:2002 Annex D-based method. One building on each farm (intervention) was cleaned and disinfected according to a rigorous protocol consisting of several steps and a Defra-approved disinfectant used at the General Orders concentration, whilst the other building (control) was cleaned and disinfected as per normal farm routine. At the post-C&D visit, Enterobacteriaceae and total bacterial counts were determined to evaluate residual faecal contamination and general hygiene levels. Rodent specialists visited the farms before and after C&D and rodent carcasses were collected for Salmonella testing. The intervention buildings were significantly less likely (p = 0.004) to be positive for Salmonella after C&D. The pre-restocking pigs had the highest likelihood (p<0.001) of being Salmonella positive (often with multiple serovars) and there was no significant difference between intervention and control buildings in Salmonella prevalence at the post-restocking visit (p = 0.199). However, the pigs housed in the intervention buildings were significantly less likely (p = 0.004) to be positive for Salmonella at slaughter age. Multivariable analysis suggested that cleaning all fixtures of buildings, leaving the pens empty for 2-3 days and using an effective disinfectant are factors significantly improving the likelihood of removing Salmonella contamination during C&D. Signs of rodents were recorded in all farms, but rodent activity and harbourage availability decreased between visits. All the rats tested were Salmonella negative. S. Typhimurium or its monophasic variants were isolated from 6 mouse carcasses in 3 farms where the same serovars were isolated from pigs. This study demonstrates that an appropriate C&D programme significantly reduces the likelihood of residual contamination in Salmonella positive pig buildings, and suggests a significant reduction in the prevalence of Salmonella in the pigs in appropriately cleaned and disinfected buildings when sampled before slaughter. Due to a high prevalence of infection in replacement pigs, control of Salmonella in pig farms is challenging. Rodents may also contribute to the carry-over of infection between batches. C&D is a useful measure to help reduce the number of infected pigs going to the slaughterhouse, but should be supplemented by other control measures along the pig breeding and production chain.

Observations on the distribution and control of Salmonella in commercial duck hatcheries in the UK

Salmonella infection causes a significant number of cases of gastroenteritis and more serious illnesses in people in the UK and EU. The serovars Salmonella Enteritidis and Salmonella Typhimurium are most frequently associated with foodborne illness in Europe. Whilst control programmes exist to monitor these serovars in the chicken and turkey sectors, no regulatory programme is currently in place for the duck sector. A voluntary industry scheme (Duck Assurance Scheme) was launched in the UK in 2010. Hatcheries act as focal points of Salmonella contamination, in particular if Salmonella-contaminated eggs from positive breeding farms enter the hatchery. Five duck hatcheries were visited in this study and four were positive for Salmonella. S. Typhimurium DT8 and S. Indiana were isolated from hatchery 1 and S. Typhimurium DT41 and S. Senftenberg were isolated from hatchery 3. S. Kottbus, S. Bovismorbificans and S. Senftenberg were isolated from hatchery 2 and S. Kedougou was isolated from hatchery 4. Advice on the control/elimination of Salmonella was provided at each visit and a longitudinal study was undertaken to monitor its effectiveness. Extensive sampling was carried out in the hatcheries visited and the tray wash area and waste/external areas had the highest probability of being contaminated. The hatcher area was also found to be a primary focus of contamination. Improvements of farm and hatchery biosecurity standards have resulted in a reduction of hatchery contamination in this study and in previous investigations. Hatcheries 1 and 5 were cleared of Salmonella, demonstrating that elimination of Salmonella contamination from duck hatcheries is achievable.

Salmonella Vaccination in Pigs: A Review

The control of Salmonella enterica in pig production is necessary for both public and animal health. The persistent and frequently asymptomatic nature of porcine Salmonella infection and the organism's abilities to colonize other animal species and to survive in the environment mean that effective control generally requires multiple measures. Vaccination is one such measure, and the present review considers its role and its future, drawing on studies in pigs from the 1950s to the present day. Once established in the body as an intracellular infectious agent, Salmonella can evade humoral immunity, which goes some way to explaining the often disappointing performance of inactivated Salmonella vaccines. More recent approaches, using mucosal presentation of antigens, live vaccines and adjuvants to enhance cell-mediated immunity, have met with more success. Vaccination strategies that involve stimulating both passive immunity from the dam plus active immunity in offspring appear to be most efficacious, although either approach alone can yield significant control of Salmonella. Problems that remain include relatively poor control of Salmonella serovars that are dissimilar to the vaccine antigen mix, and difficulties in measuring and predicting the performance of candidate vaccines in ways that are highly relevant to their likely use in commercial production.

Estimation of the sensitivity of various environmental sampling methods for detection of Salmonella in duck flocks

Reports of Salmonella in ducks in the UK currently rely upon voluntary submissions from the industry, and as there is no harmonized statutory monitoring and control programme, it is difficult to compare data from different years in order to evaluate any trends in Salmonella prevalence in relation to sampling methodology. Therefore, the aim of this project was to assess the sensitivity of a selection of environmental sampling methods, including the sampling of faeces, dust and water troughs or bowls for the detection of Salmonella in duck flocks, and a range of sampling methods were applied to 67 duck flocks. Bayesian methods in the absence of a gold standard were used to provide estimates of the sensitivity of each of the sampling methods relative to the within-flock prevalence. There was a large influence of the within-flock prevalence on the sensitivity of all sample types, with sensitivity reducing as the within-flock prevalence reduced. Boot swabs (individual and pool of four), swabs of faecally contaminated areas and whole house hand-held fabric swabs showed the overall highest sensitivity for low-prevalence flocks and are recommended for use to detect Salmonella in duck flocks. The sample type with the highest proportion positive was a pool of four hair nets used as boot swabs, but this was not the most sensitive sample for low-prevalence flocks. All the environmental sampling types (faeces swabs, litter pinches, drag swabs, water trough samples and dust) had higher sensitivity than individual faeces sampling. None of the methods consistently identified all the positive flocks, and at least 10 samples would be required for even the most sensitive method (pool of four boot swabs) to detect a 5% prevalence. The sampling of dust had a low sensitivity and is not recommended for ducks.

A longitudinal observational study of Salmonella shedding patterns by commercial turkeys during rearing and fattening, showing limitations of some control measures

1. The onset and progression of Salmonella infections was investigated in commercial turkey flocks from placement at 1 d old until slaughter in "brood and move" systems using a longitudinal observational approach based on faeces and environmental sampling with subsequent culture of Salmonella. 2. Persistent Salmonella Newport contamination was found within rearing houses and on their external concrete aprons after cleaning and disinfection between crops of heavily shedding young birds. 3. Salmonella shedding was often detected by 5 d of age and the frequency of positive samples peaked at 14-35 d. Thereafter Salmonella isolations declined, especially in the later (fattening) stages. Samples were still Salmonella-positive at low prevalence in half of the intensively sampled houses at slaughter age. 4. A number of management interventions to combat Salmonella infection of flocks, including sourcing policy, competitive exclusion cultures and cleaning and disinfection, were inadequate to prevent flock infection, although improved disinfection on one unit was associated with a delay in the onset of flock infection.

Assessment of producers' response to Salmonella biosecurity issues and uptake of advice on laying hen farms in England and Wales

High standards of biosecurity are known to reduce the risk of disease outbreaks; however, uptake of advice and implementation of biosecurity measures are dependent on many factors. This study assessed the uptake of targeted biosecurity advice by 60 laying hen farms provided during biosecurity audit visits. Advice was provided as bullet point cards focusing on specific areas identified as benefitting from improvement. These covered site entrance, site tidiness, vaccination, boot hygiene, hand hygiene, house tidiness, rodent control, fly control, red mite control and cleaning and disinfection between flocks. Background knowledge of Salmonella and biosecurity and farmers' willingness and intent to implement additional measures were assessed. About 50% of the principal decision-makers had basic background knowledge of Salmonella, with 22% considered well informed; almost all agreed that biosecurity could impact on Salmonella control and many appeared willing to implement additional biosecurity measures. Sixty-three per cent of study farms were categorised using the Defra Farmer Segmentation Model as Modern Family Businesses (MFBs), with 7-11% of farms being categorised as Custodian, Lifestyle Choice, Pragmatist or Challenged Enterprise; however, categorisation, did not determine uptake of advice. The most frequently used advice cards were boot hygiene, red mite control, hand hygiene, site entrance and cleaning and disinfection; uptake of advice ranged from 54 to 80% depending on the advice card. Uptake of advice by the farmers was encouraging, especially considering it was being provided by people other than their usual source of biosecurity information. Those who did not implement the recommended measures cited cost, difficulty of enforcement and practicality as the main reasons. However, the positive uptake of advice and implementation of recommended measures by many farmers demonstrates that targeted advice, discussed face to face with farmers, on a small number of key areas, is a potentially effective method of providing biosecurity information to complement more lengthy formal advisory reports.

Salmonella enterica serovar Enteritidis, England and Wales, 1945-2011

A focus on eliminating phage type 4 in egg and poultry production has greatly reduced foodborne disease among humans.

In England and Wales, the emergence of Salmonella enterica serovar Enteritidis resulted in the largest and most persistent epidemic of foodborne infection attributable to a single subtype of any pathogen since systematic national microbiological surveillance was established. We reviewed 67 years of surveillance data to examine the features, underlying causes, and overall effects of S. enterica ser. Enteritidis. The epidemic was associated with the consumption of contaminated chicken meat and eggs, and a decline in the number of infections began after the adoption of vaccination and other measures in production and distribution of chicken meat and eggs. We estimate that >525,000 persons became ill during the course of the epidemic, which caused a total of 6,750,000 days of illness, 27,000 hospitalizations, and 2,000 deaths. Measures undertaken to control the epidemic have resulted in a major reduction in foodborne disease in England and Wales.

A review of the official sampling of flocks of laying hens in the Salmonella National Control Programme in Great Britain

In line with European legislation and the UK National Control Programme for Salmonella, poultry farms are sampled to establish their Salmonella status. Regular samples are collected by the farmer (operator), with annual routine (official) samples being collected by the competent authority to verify achievement of the Salmonella programme reduction target. To confirm sampling was being carried out effectively, a questionnaire-based survey was conducted. The aim was to identify any complicating factors the samplers encountered and the decisions made in these circumstances. There was good compliance with the official sampling visits, with few delays reported. However, farm-specific clothing/separate boots for non-caged houses were rarely provided by the operator, whereas boot dips and hand washing facilities were usually available. The collection of dust was often a problem for official samplers, operator boot swabs were not always moistened before sampling and both sampler groups did not always follow the recommended method for the collection of faeces from belts and scrapers. Overall, there was a good application of the sampling protocol, although a few areas for improvement were identified.

Characteristics of ciprofloxacin and cephalosporin resistant Escherichia coli isolated from turkeys in Great Britain

1. A field study was performed to investigate the presence and characteristics of ciprofloxacin-resistant, extended spectrum β-lactamase (ESBL) and AmpC Escherichia coli from turkeys in Great Britain. E. coli were isolated from ~9000 boot swab samples from 27 different farms owned by four different companies. Between 1 and 14 visits were made to each farm (mean 3) at between 0 and 15 m intervals (mean ~5 m). 2. CHROMagar ECC with and without ciprofloxacin or cephalosporin antibiotics was used as selective isolation media. Representative isolates with different phenotypes were tested for mutations in gyrA and for: qnrA, B, S, qepA and aac(6')-Ib genes, for ESBL phenotype, the presence of bla genes and plasmid type, and for ampC genes Representative ciprofloxacin-resistant and CTX-M isolates were further tested for serotype and PFGE type. On ciprofloxacin selective media 55% of samples yielded ciprofloxacin resistant E. coli and of those further analysed, most had ciprofloxacin MICs >4 mg/l and mutations in gyrA. 3. For the different companies, the mean number of samples per farm with cefoxitin- or cefotaxime-resistant isolates ranged from 1·0% to 61·9% and 4·7% to 31·7% respectively. Cefotaxime-resistance was most commonly associated with an ESBL phenotype, a CTX-M-1 or CTX-M-14 sequence type and an I1-γ or K plasmid inc type. The mechanism of cefoxitin resistance was not determined for most isolates, but where determined it was bla . 4. PFGE and serotyping showed clonally-related isolates persisting over multiple visits suggesting both more prudent use of antibiotics and improved farm hygiene are needed to address the issue of antimicrobial resistance in isolates from turkeys.

Survey of Salmonella prevalence on commercial turkey breeding and fattening farms in the UK in 2006 to 2007

A total of 29 breeding turkey holdings and 317 fattening turkey holdings were sampled between October 2006 and September 2007 in order to establish the baseline prevalence of Salmonella in turkeys in the UK. The weighted holding level Salmonella prevalence was found to be 20.1 per cent (95 per cent confidence interval [CI] 8.6 to 40.3 per cent) in breeding turkeys and 37.7 per cent (95 per cent CI 33.4 to 42.3 per cent) in fattening turkeys. For breeding turkeys, a weighted flock-level prevalence, as more than one flock per holding was sampled, was estimated at 7.1 per cent (95 per cent CI 3.2 to 14.8 per cent). A total of 13 different serovars were identified in the survey. The most frequent serovar in both turkey flock classes was Salmonella Kottbus, which was found on two breeding holdings and 63 of the fattening holdings giving weighted prevalences of 10.4 per cent (95 per cent CI 2.6 to 34.1 per cent) and 23.0 per cent (95 per cent CI 19.3 to 27.3 per cent), respectively. On breeding holdings, a single isolate of Salmonella Typhimurium, identified as DT12 (weighted prevalence 3.5 per cent [95 per cent CI 0.7 to 15.8 per cent] [holding], 0.7 per cent [95 per cent CI 0.1 to 3.7 per cent] [flock)], was found. On fattening holdings, there were 55 isolates of S Typhimurium from 16 holdings, giving a weighted prevalence of this serovar of 5.4 per cent (95 per cent CI 3.6 to 8.0 per cent). There were no isolates of Salmonella serovars Enteritidis, Hadar, Infantis or Virchow.

A critical review of Salmonella Typhimurium infection in laying hens

Salmonella Typhimurium has been reported to contaminate egg production across the world, but where Salmonella Enteritidis is endemic it is this latter serovar that dominates egg-borne salmonellosis. However, Salmonella Typhimurium is a major food-borne pathogen so it is important to understand how it can impact the microbiological safety of eggs and what serovar-specific control strategies may be appropriate in the future as control over Salmonella Enteritidis continues to improve. To that end, the present review examines the published literature on Salmonella Typhimurium in laying hens and eggs, with particular reference to comparative studies examining different serovars. Experimentally Salmonella Enteritidis is more often isolated from egg contents and seems to adhere better to reproductive tract mucosa, whilst Salmonella Typhimurium appears to provoke a more intense tissue pathology and immune response, and flock infections are more transient. However, it is observed in many cases that the present body of evidence does not identify clear differences between specific behaviours of the serovars Typhimurium and Enteritidis, whether in laying hens, in their eggs, or in the laying environment. It is concluded that further long-term experimental and natural infection studies are needed in order to generate a clearer picture.

Producing Salmonella-free pigs: a review focusing on interventions at weaning

Salmonella infection in pig production is typically endemic and largely asymptomatic. It is a cause of substantial concern among food safety bodies, prompting voluntary and legislative responses aimed at monitoring and reducing the number of Salmonella-infected animals entering the human food chain. Elimination of the problem at an early stage of production is highly desirable, and to this end the present review examines published evidence on the carriage of Salmonella by piglets before and after weaning, as well as evidence on the dynamics of Salmonella infection in the weaner and grower stages of pig production, the effects of maternal immunity, and risk factors for Salmonella excretion after weaning. Various interventions to reduce or eliminate Salmonella infection in young pigs have been tried, such as vaccination, competitive exclusion, treatments in feed and water, antibiotic administration, disinfection of animals, and segregated weaning to clean accommodation. The evidence on the effectiveness of these is considered, and the last is examined in some detail, as it appears currently to offer the best chance of eliminating Salmonella from growing stock.

Salmonella serovars and antimicrobial resistance patterns on a sample of high seroprevalence pig farms in England and Wales (2003-2008)

Following the introduction of a national abattoir-based monitoring programme for Salmonella in pigs, advisory visits were made to pig farms in England and Wales with high Salmonella seroprevalence assessed by muscle tissue fluid (meat juice) ELISA. Samples (n = 15 790), including pooled pen floor faeces (n = 12 136), were collected for Salmonella culture from 296 farms, between October 2003 and February 2008. Salmonella was isolated from 4489 (28%) of all samples collected, including 3301 (27%) of pooled pen floor faecal samples, from 270 (91%) of farms visited. Salmonella Typhimurium and S. Derby were the most prevalent serovars, representing 64% and 16% of isolates serotyped, respectively. The main phage types of S. Typhimurium identified were U288 and DT193. Antimicrobial resistance (AMR) was seen in 92% of isolates tested, with the highest frequencies of resistance occurring to tetracyclines (T), sulphonamide compounds (SU), ampicillin (AM), sulphamethoxazole/trimethoprim (SXT), streptomycin (S) and chloramphenicol (C). Fifty-nine AMR patterns were observed, the most frequent of these being T, AM, SXT, C, S, SU, seen in 35% of isolates tested. Multi-drug resistance was commonly found, with 67% of isolates submitted for AMR testing showing resistance to between four and nine antimicrobials.

Use of multiple-locus variable-number tandem-repeats analysis (MLVA) typing to characterize Salmonella Typhimurium DT41 broiler breeder infections

AIMS

To characterize isolates of Salmonella Typhimurium DT41 obtained from infected flocks of broiler breeders by multiple-locus variable-number tandem-repeats analysis (MLVA) and compare results with a diverse strain collection from Germany and United Kingdom and isolates from Danish patients.

METHODS AND RESULTS

A total of 102 isolates of Salm. Typhimurium phage type DT41 were MLVA typed. MLVA typing showed 4, 12, 25, 9 and 8 different alleles at the five MLVA loci 9, 5, 6, 10 and 3, respectively. A dendrogram based on MLVA types was constructed, and one large group, nine minor groups and 29 more unrelated MLVA types were obtained. The major group included 20 of the 30 human isolates. Isolates obtained from broiler breeders demonstrated major diversity, indicating the existence of several independent introductions of DT41 at farm level. When comparison was made to isolates included from Germany and England, DT41 seems to be ubiquitous in the wild fauna which might represent a risk factor for poultry.

CONCLUSIONS

Transmission from Danish broilers to humans was not demonstrated, neither was the transmission from rearing farms to broiler breeder farms. Sources of infection at broiler breeder farm level remained unidentified.

SIGNIFICANCE AND IMPACT OF THE STUDY

Major diversity was demonstrated for DT41 MLVA types. A persisting problem with infection of broiler breeder flocks with DT41 was not reflected in broiler flocks originating from these flocks.

The impact of different housing systems on egg safety and quality

A move from conventional cages to either an enriched cage or a noncage system may affect the safety or quality, or both, of the eggs laid by hens raised in this new environment. The safety of the eggs may be altered either microbiologically through contamination of internal contents with Salmonella enterica serovar Enteritidis (Salmonella Enteritidis) or other pathogens, or both, or chemically due to contamination of internal contents with dioxins, pesticides, or heavy metals. Quality may be affected through changes in the integrity of the shell, yolk, or albumen along with changes in function, composition, or nutrition. Season, hen breed, flock age, and flock disease-vaccination status also interact to affect egg safety and quality and must be taken into account. An understanding of these different effects is prudent before any large-scale move to an alternative housing system is undertaken.

Salmonella infection in cattle in Great Britain, 2003 to 2008

Surveillance data for clinical disease in cattle in Great Britain due to Salmonella infections were analysed for the period 2003 to 2008 in order to describe seasonality and to investigate possible associations between Salmonella diagnoses and other variables such as region, climate, age and production type. A clear seasonal pattern was shown for Salmonella infection, coinciding with the second half of the year. The incidence of Salmonella Dublin and Salmonella Typhimurium was highest in the west of the country, which has the greatest cattle density, but this was not a feature of diagnoses with other serovars. Abortion was a more common clinical sign of S Dublin infections, but was relatively unusual in the case of S Typhimurium. The observed clinical picture and age of affected animals were largely determined by the seasonality of dairy cattle calving in Great Britain.

Review of the carriage of zoonotic bacteria by arthropods, with special reference to Salmonella in mites, flies and litter beetles

This systematic review considers the relationship between arthropods commonly found in and around livestock premises and zoonotic bacteria. The principal focus is upon insects and arachnids on poultry units, where houses, litter and manure provide good conditions for the growth, multiplication and protection of flies, beetles and mites, and where zoonotic pathogens such as Salmonella and Campylobacter are prevalent. Other members of the Enterobacteriaceae and the taxa Clostridium, Helicobacter, Erysipelas and Chlamydiaceae are also discussed. Salmonella is widely distributed in the flies of affected livestock units and is detectable to a lesser degree in beetles and mites. Persistent carriage appears to be common and there is some field and experimental evidence to support arthropod-mediated transmission between poultry flocks, particularly carry-over from one flock to the next. Campylobacter may readily be isolated from arthropods in contact with affected poultry flocks, although carriage is short-lived. There appears to be a role for flies, at least, in the breaching of biosecurity around Campylobacter-negative flocks. The carriage of other zoonotic bacteria by arthropods has been documented, but the duration and significance of such associations remain uncertain in the context of livestock production.

Chemical treatment of animal feed and water for the control of Salmonella

The control of Salmonella in animal feedstuffs is important, principally to protect the human food chain from contamination by Salmonella derived from infected animals. The transmission of Salmonella from animal feeds to animals, and onward to human food products, has been convincingly documented. This is especially important for chicken breeding and laying flocks and pigs, in view of the consequences of recent or imminent control legislation in the European Union. Animal feed ingredients, particularly animal and plant-derived protein meals, are frequently contaminated with Salmonella either from source or from processing plant, and recontamination in compounding mills is an additional problem. Several complementary strategies have been used to control this feed contamination, and these include a range of chemical treatments. The principal agents used are as follows: organic acids and their salts, formaldehyde, and bacterial membrane disruptors such as terpenes and essential oils. Experimental agents include chlorate compounds. Many products use blends of agents from the same or different chemical groups to achieve synergistic or combination effects. The present review draws upon published and company data to describe the various modes of action and efficacies of different chemical agents delivered in feed or in drinking water against Salmonella occurring in feed or in livestock environments. Reasons for the failure of protection are explored, along with problems in usage such as corrosion and reduced palatability. Given the wide array of products available with contrasting modes of action, the need for standardized tests of efficacy is also discussed.

Retrospective analysis of Salmonella isolates recovered from animal feed in Great Britain

To examine feed contamination rates with Salmonella, the diversity of serovars and the antimicrobial resistance of isolates from animal feedingstuffs in Great Britain, and to compare Salmonella strains found in animal feed and in livestock, data collected under voluntary and statutory Salmonella surveillance during the period 1987 to 2006 were analysed retrospectively. The feed contamination rate decreased from 3.8 per cent in 1993 to 1.1 per cent in 2006. A total of 263 Salmonella serovars were recovered: S Mbandaka (11.2 per cent), S Tennessee (10.4 per cent), S Senftenberg (8.4 per cent), S Agona (6.4 per cent), S Montevideo (6.4 per cent) and S Ohio (3.1 per cent) were the most prevalent. S Typhimurium was recovered at a proportion of 1.6 per cent from raw ingredients and 2.4 per cent from finished feed, while S Enteritidis was recovered at a proportion of 0.5 per cent from raw ingredients and 0.6 per cent from finished feed; 14.1 per cent of the isolates were resistant to at least one antimicrobial, and 1.9 per cent were multiresistant. There was no evidence of a statistical association (P<0.05) between the top 10 serovars recovered from feed and from livestock.

Sampling and bacteriological detection of Salmonella in poultry and poultry premises: a review

The detection of Salmonella in primary poultry production is an issue of great concern in the European Union (EU), since control of this zoonotic disease is in part based on the reduction of the prevalence at the farm level. Success of detection is likely to be highly dependent on the choice of an adequate sampling procedure combined with a sensitive culture method. In poultry farms 'naturally pooled' faeces/litter and dust are the matrices of choice. In floor systems boot swabs are the preferred method for the collection of faeces. A wide range of culture methods is available, but ISO 6579:2002 (Annex D) is currently the standard for poultry environmental samples in the EU. In this review, the authors discuss in detail the range of sampling and culture methodologies for Salmonella in poultry farms. The review also covers sampling and testing of poultry hatcheries, live birds and poultry carcasses.

Comparison of sampling methods to detect Salmonella infection of turkey flocks

AIMS

To compare the efficiency of various sampling methods for detection of Salmonella in turkey flocks.

METHODS AND RESULTS

In a field study that compared various sampling methods one pair of boot swabs taken from the whole turkey house provided suitably sensitive results for fattening and rearing flocks and was no less sensitive than two pairs, each from half the house, tested as a pooled sample. The sensitivity was further enhanced by adding a dust sample. The dust sample appeared to be particularly useful in flocks with a low prevalence, especially in breeding flocks, and was more sensitive than a method which used five pairs of boot swabs per flock. Combined incubation of a boot swab and a dust sample showed no interference between the two sample types and a maximum sensitivity of detection. Litter samples and commercial sponge drag swabs provided a lower level of detection.

CONCLUSIONS

A single pair of boot swabs taken from the whole house is recommended for routine sampling of commercial rearing or fattening flocks. An additional dust sample could be added to increase detection in flocks with a low prevalence or in breeding flocks, but adding an additional pair of boot swabs would not increase detection compared with a single pair.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study demonstrates that significant efficiencies can be made in sampling programmes for detection of Salmonella in turkey flocks without detracting from the sensitivity. Similar studies are recommended for other poultry sectors, particularly in chicken breeding flocks.

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.