A food chain approach to control of Shiga toxin-producing Escherichia coli in New Zealand : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Veterinary Science at Massey University, Palmerston North, New Zealand

Part of Chapter 3 has been published as: Browne, A.S., Midwinter, A.C., Withers, H., Cookson, A.L., Biggs, P.J., Marshall J.C., Benschop, J., Hathaway, S., Haack, N., Akhter, R., & French, N.P. (2018). Molecular epidemiology of Shiga toxin-producing Escherichia coli (STEC) on New Zealand dairy farms: Application of a culture-independent assay and whole-genome sequencing. Applied and Environmental Microbiology, 84(14). DOI: 10.1128/AEM.00481-18This thesis describes the prevalence and molecular epidemiology of Shiga toxin-producing Escherichia coli (STEC) in New Zealand using microbiological, genomic, molecular, and statistical methods. STEC are a zoonotic pathogen that can cause bloody diarrhoea and acute kidney failure. Cattle are a well-recognized STEC reservoir, and previous research has identified living near cattle and contact with their faeces as an increased risk for human infection. Seven STEC serogroups (O157, O26, O45, O103, O111, O121, O145), known as the ‘Top 7’ STEC, have been identified as an increased risk to human health, with the New Zealand meat industry undertaking testing to ensure that veal beef exports to some international markets are free of these ‘Top 7’ serogroups. A random stratified cross-sectional study of ‘Top 7’ STEC prevalence of young dairy calves (n=1,508) on New Zealand dairy farms (n=102) found that approximately 20% of calves and 75% of farms were positive for one or more of the ‘Top 7’ STEC. ‘Top 7’ STEC prevalence was positively associated with increased number of calves in a calf pen, and prevalence significantly varied by region. This study utilized a new culture-independent diagnostic test, NeoSEEK (PCR/MALDI-TOF method), and used statistical and microbiological techniques to evaluate the sensitivity and specificity of the method for this and further studies. A longitudinal study evaluating prevalence and transmission of ‘Top 7’ STEC in animals and the dairy farm environment found evidence of calf-to-calf, dam-to-calf, and environment-to-calf transmission. Whole genome sequencing analysis and prevalence data revealed cross-contamination of young veal calf hides occurs during transport and lairage to processing plants. Analysis of New Zealand serogroup O26 bacterial isolates (n=152), in comparison to publicly available genome sequence data (n=252) from other countries (n=14), suggested introduction of STEC and non-STEC O26 into New Zealand during few periods in the 20th and early 21st century. Populations of New Zealand serogroup O26 E. coli are monophyletic, possibly due to minimal live cattle importations into the country. Further research in this area should focus on effective interventions at the farm and meat processing level to decrease the risk of veal beef contamination, while protecting public health

Performance of the resurfaced hip. Part 1: the influence of the prosthesis size and positioning on the remodelling and fracture of the femoral neck

Hip resurfacing is an established treatment for osteoarthritis in young active patients. Failure modes include femoral neck fracture and prosthesis loosening, which may be associated with medium-term bone adaptation, including femoral neck narrowing and densification around the prosthesis stem.Finite element modelling was used to indicate the effects of prosthesis sizing and positioning on the bone remodelling and fracture strength under a range of normal and traumatic loads, with the aim of understanding these failure modes better.The simulations predicted increased superior femoral neck stress shielding in young patients with small prostheses, which required shortening of the femoral neck to give an acceptable implant–bone interface. However, with a larger prosthesis, natural femoral head centre recreation in the implanted state was possible; therefore stress shielding was restricted to the prosthesis interior, and its extent was less sensitive to prosthesis orientation. With valgus orientation, the implanted neck strength was, at worst, within 3 per cent of its intact strength.The study suggests that femoral neck narrowing may be linked to a reduction in the horizontal femoral offset, occurring if the prosthesis is excessively undersized. As such, hip resurfacing should aim to reproduce the natural femoral head centre, and, for valgus prosthesis orientation, to avoid femoral neck fracture

Epidemiology of blood donor health in the context of increased frequency of donation: The INTERVAL trial

Blood donation is central to maintaining adequate blood supply for routine hospital demands and ensuring preparedness for emergency situations. As blood donation is a voluntary activity, it is important that blood collection services ensure that blood donor health is not negatively impacted in the strive to maintain blood supply. However, health-related consequences of frequent blood donation are not fully understood, and the relevance of iron supplementation remains unclear. Thus, the aim of this thesis was to investigate different aspects of blood donor health (including quality of life, iron levels and symptoms related to iron deficiency) and to summarise key characteristics of donors who may be able to safely give blood donations more frequently. The INTERVAL trial was a large pragmatic trial conducted to assess whether blood supply in the UK could be safely increased by reducing the interval between blood donations. A total of 45,263 UK blood donors (50% men and 50% women) were assigned to donate blood more frequently (men: 8 and 10 weeks; women: 12 and 14 weeks) than routine practice (men: 12 weeks, women 16 weeks). Interactions with randomised inter-donation interval were assessed to identify donor subgroups who may safely donate more frequently without affecting the trial’s key safety outcome - low haemoglobin deferrals. Mediation analyses were performed to assess whether iron supplementation during the trial mediated the effect of randomised inter-donation frequency on donor reported symptoms potentially associated with iron deficiency, including tiredness, breathlessness, palpitations, and fainting. Modelling was performed to assess the effect of more frequent blood donation on donors’ physical and mental wellbeing. Among 252,528 donor attendances during the 2-year period of the INTERVAL trial, 222,370 (88%) resulted in successful donation and 13,099 (5%) resulted in low haemoglobin deferrals. Donors randomised to shorter inter-donation intervals were able to give more donations, but also had higher frequency of low haemoglobin deferrals. Further interaction analyses conducted in this thesis suggested that increased frequency of donations with shorter inter-donation intervals was modified by age, donation history, iron multivitamin supplement use, physical and mental health scores and ferritin levels. The effect of randomised inter-donation interval on low haemoglobin deferrals was modified by baseline donation history, age, haemoglobin level and ferritin level. Donors randomised to shorter inter-donation intervals reported higher frequencies of symptoms such as tiredness, breathlessness, fainting or feeling faint, and palpitations. Use of iron supplementation, a commonly studied therapy for relieving symptoms such as fatigue, also increased during the trial. However, the effect of shorter inter-donation intervals on the frequency of symptoms was the same irrespective of adjustment for iron supplementation use before or during the trial. Donors in the INTERVAL trial had higher physical and mental health component scores (PCS, MCS) than the general population. While the PCS and MCS were associated with baseline characteristics such as age, weight, and previous diagnosis of anaemia, there was no significant effect of randomised inter-donation interval on any of PCS, MCS, or the eight sub-components that make up the two summary measures. The findings from this thesis may help inform future directions for blood donation practice and management in the UK and elsewhere. Characteristics of donors able to safely donate blood more frequently and those who may be at greater risk of low haemoglobin deferrals were identified. Impact on donors’ quality of life appears marginal. Some physical symptoms may be experienced by donors who donate more frequently, irrespective of iron supplementation use, suggesting need for further study to elucidate other mechanisms of mitigating post-donation symptoms

Guaranteed energy-efficient bit reset in finite time

Landauer's principle states that it costs at least kTln2 of work to reset one bit in the presence of a heat bath at temperature T. The bound of kTln2 is achieved in the unphysical infinite-time limit. Here we ask what is possible if one is restricted to finite-time protocols. We prove analytically that it is possible to reset a bit with a work cost close to kTln2 in a finite time. We construct an explicit protocol that achieves this, which involves changing the system's Hamiltonian avoiding quantum coherences, and thermalising. Using concepts and techniques pertaining to single-shot statistical mechanics, we further develop the limit on the work cost, proving that the heat dissipated is close to the minimal possible not just on average, but guaranteed with high confidence in every run. Moreover we exploit the protocol to design a quantum heat engine that works near the Carnot efficiency in finite time.Comment: 5 pages + 5 page technical appendix. 5 figures. Author accepted versio

Cow, farm, and herd management factors in the dry period associated with raised somatic cell counts in early lactation

This study investigated cow characteristics, farm facilities, and herd management strategies during the dry period to examine their joint influence on somatic cell counts (SCC) in early lactation. Data from 52 commercial dairy farms throughout England and Wales were collected over a 2-yr period. For the purpose of analysis, cows were separated into those housed for the dry period (6,419 cow-dry periods) and those at pasture (7,425 cow-dry periods). Bayesian multilevel models were specified with 2 response variables: ln SCC (continuous) and SCC >199,000 cells/mL (binary), both within 30 d of calving. Cow factors associated with an increased SCC after calving were parity, an SCC >199,000 cells/mL in the 60 d before drying off, increasing milk yield 0 to 30 d before drying off, and reduced DIM after calving at the time of SCC estimation. Herd management factors associated with an increased SCC after calving included procedures at drying off, aspects of bedding management, stocking density, and method of pasture grazing. Posterior predictions were used for model assessment, and these indicated that model fit was generally good. The research demonstrated that specific dry-period management strategies have an important influence on SCC in early lactation

The Other Beetle-Hunter

History of Scienc

The Effects of Fatty Desposits on the Accuracy of the Fibroscan Liver Transient Elastography Ultrasound System

A new generation of ultrasound transient elastography (TE) systems have emerged which exploit the well-known correlation between the liver’s pathological and mechanical properties through measurements of the Young’s elastic modulus; however, little work has been carried out to examine the effect that fatty deposits may have on the TE measurement accuracy. An investigation was carried out on the effects on the measurement accuracy of a transient elastography ultrasound system, the Fibroscan®, caused by overlaying fat layers of varying thickness on healthy liver-mimicking phantoms, simulating in vivo conditions for obese patients. Furthermore, a steatosis effect similar to that in non-alcoholic fatty liver disease (NAFLD) and alcoholic liver disease (ALD) was simulated to investigate its effect on the TE system. A range of novel elastography fat-mimicking materials were developed using 6-10wt% poly(vinyl alcohol) cryogel capable of achieving a range of acoustic velocities (1482-1530m/s) and attenuation coefficients (0.4-1dB/MHz/cm) for simulating different liver states. Laboratory-based acoustic velocities and attenuation coefficients were measured while the Young’s modulus was established through a gold standard compression testing method. A significant variation of the Young’s elastic modulus was measured in healthy phantoms with overlaying fat layers of thicknesses exceeding 45mm, impinging on the scanners region of interest, overestimating the compression tested values by up to 11kPa in some cases. Furthermore, Fibroscan® measurements of the steatosis phantoms showed a consistent overestimation (~54%), which strongly suggests that the speed of sound mismatch between that of liver tissue and that assumed by the scanner is responsible for the high clinical cut-offs established in the case of ALD and NAFLD

Evaluation of CIRS String Doppler Phantom as a Test Tool for Use in a Doppler Ultrasound Quality Assurance Program

Ultrasound Doppler systems are routinely used to perform blood flow velocity measurements which assist in the clinical assessment and diagnosis of vascular. Doppler measurements of peak velocities for vascular applications provide an indication of the degree of the stenosis which will ultimately assist in deciding how a patient is managed. It is imperative that Doppler systems are capable of accurately measuring blood flow velocities to ensure correct diagnosis and appropriate patient treatment; therefore such systems should be evaluated regularly as part of a Quality Assurance program. Although a range of Doppler test phantoms have been developed for quality control (QC) purposes to establish the measurement accuracy and stability of Doppler systems only a limited number of such test phantoms are commercially available, the easiest of these devices to operate is the String Phantom. Currently, only one string Doppler phantom is commercially available, namely the CIRS Model 043. In this study an evaluation of the performance of this test device was carried out as a number of problems currently exist with it such as the filament type, the fact that the filament passes through a water–air interface and vibrations from the motor. This study has established that the braided-silk filament, provided with the phantom, should not be used as it introduces errors of as much as 24% for the mean velocity accuracy and 20% for the intrinsic spectral broadening (ISB) depending on the soak time of the filament. Rather, to avoid such errors it is advised that the phantom be retrofitted with a filament made from an O-ring rubber. While this eliminates the temporal changes in backscatter seen with the braided-silk filament, further discrepancies were observed, even with an O-ring filament, when the filament velocity was set in the range 26–44 cm/s, where a resonance effect significantly increased the variability of the maximum velocity accuracy and ISB measurements. This was most likely as a result of the imposed vibrations from the motor, which is mounted directly onto the tank wall; hence, it would prove practical to avoid taking measurements in this velocity range where resonance effects are observed

Review of Ultrasound Elastography Quality Control and Training Test Phantoms

While the rapid development of ultrasound elastography techniques in recent decades has sparked its prompt implementation in the clinical setting adding new diagnostic information to conventional imaging techniques, questions still remain as to its full potential and efficacy in the hospital environment. A limited number of technical studies have objectively assessed the full capabilities of the different elastography approaches, perhaps due, in part, to the scarcity of suitable tissue-mimicking materials and appropriately designed phantoms available. Few commercially-available elastography phantoms possess the necessary test target characteristics or mechanical properties observed clinically, or indeed reflect the lesion-to-background elasticity ratio encountered during clinical scanning. Thus, while some phantoms may prove useful, they may not fully challenge the capabilities of the different elastography technniques, proving limited when it comes to quality control (QC) and/or training purposes. Although a variety of elastography tissue-mimicking materials, such as agar and gelatine dispersions, co-polymer in oil and poly(vinyl) alcohol cryogel, have been developed for specific research purposes, such work has yet to produce appropriately designed phantoms to adequately challenge the variety of current commercially-available elastography applications. Accordingly, there is a clear need for the further development of elastography TMMs and phantoms to keep pace with the rapid developments in elastography technology, to ensure the performance of these new diagnostic approaches are validated, and for clinical training purposes

Characterisation of the Colour Doppler Twinkle Artefact

This investigation involved the development of a range of Colour Doppler Twinkle Artefact phantoms to characterise and quantify the “Twinkle” artefact which is often present when an irregular structure is encountered in the imaged field of view. The artefact occurs in both colour and power Doppler ultrasound imaging and manifests as a false depiction of colour velocity information in stationary soft tissue and therefore can cause significant misdiagnosis of areas of flow within the patient. It has been hypothesised that it is generated due to a strongly reflecting medium composed of individual reflectors and therefore becomes a clinical concern when parenchymal calcifications are encountered. (Tsao et al., 2006). The aim of this study was to investigate the occurrence and magnitude of this artefact across a range of ultrasound scanners and to monitor the effects on the artefact of varying image acquisition parameters. A range of phantoms were produced that could reproducibly recreate the Twinkle artefact, the presence of which was quantified in a range of scanners (Zonare, Siemens Antares, Philips HDI and IU22). These phantoms included both fine and coarse structures as well as a flow channel in one of the phantoms, through which blood mimicking fluid was pumped. A semi-quantitative grading system was implemented and instrument controls such as pulse repetition frequency (PRF), colour write priority, greyscale gain and depth of focal zone were varied in order to determine their impact on the Twinkle artefact. Instrument control settings were found to significantly affect the intensity of this artefact, predominantly PRF showed a significant increase in the presence of this artefact. Furthermore, the extent of the artefact varied greatly across the range of scanners with Siemens Antaries and Zonare being most sensitive to the artefact. The implication of this study has shown the Twinkle artefact to be dependent on scanner specifications and instrumental parameters. With careful image optimisation, a reduction or elimination of the artefact can be achieved