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1.
N Z Vet J ; 68(3): 150-156, 2020 May.
Article in English | MEDLINE | ID: mdl-31973682

ABSTRACT

This review outlines the processes followed by New Zealand Thoroughbred Racing (NZTR) when developing its Thoroughbred Welfare Assessment Guidelines. It accepted that guidance on welfare management must be based on up-to-date knowledge of how animal welfare is understood scientifically. NZTR established an expert panel to facilitate this process. First, major changes in animal welfare science thinking over the last 40 years were considered. For example, the separate biological function and affective state orientations were later accepted as dynamically interacting elements within the body operating as an integrated whole entity; conceptual problems with the Five Freedoms framework led to the formulation of the Five Provisions and Welfare Aims paradigm and development of the Five Domains Model for assessing nutritional, environmental, health, behavioural and mental facets of animal welfare; and the initial major focus on negative experiences evolved to include both negative and positive experiences. The Five Domains Model was very effective for illustrating up-to-date understanding of animal welfare and its use demonstrated how comprehensive animal welfare assessments may be conducted. The NZTR panel followed a sequential approach that included an update on animal welfare thinking and the Five Provisions and Welfare Aims paradigm; the generic Five Domains Model was refocused specifically on equids; a detailed model assessment of equine welfare practices was conducted; enhanced equine welfare practices were emphasised by comparing them to inadequate welfare practices; guidelines were framed in terms which provide domain-specific advice on provisions that achieve positive welfare; other domain-specific guidelines were focused on welfare-compromising consequences of inadequate provisions; and welfare-appropriate conditions were clarified for all stages of a Thoroughbred's life cycle (in work and rest) to facilitate exercising a life-long duty of care. Finally, the guidelines were expressed in general terms to avoid them becoming overly detailed and unwieldy. They therefore do not address specific welfare issues such as use of whips, bits, spurs and tight nosebands, however the Five Domains Model may also be used for these specific purposes. The guidelines, and the way they were formulated, provide an example of one approach which other organisations may find immediately useful, or which may stimulate them to devise their own approaches when progressing such equine welfare initiatives.


Subject(s)
Animal Husbandry , Animal Welfare , Guidelines as Topic , Horses , Animal Husbandry/methods , Animal Husbandry/standards , Animal Welfare/standards , Animals , Evidence-Based Practice , Humans , New Zealand
2.
N Z Vet J ; 68(1): 65-68, 2020 Jan.
Article in English | MEDLINE | ID: mdl-31554484

ABSTRACT

Case History: Two calves delivered following elective caesarean section showed behaviour typical of neonatal maladjustment syndrome described in foals, i.e., indifference to environmental stimuli, lack of affinity for the dam, failure to find the udder, refusal to suck, aimless wandering or motionless standing. Calves were subjected to a clinical examination immediate after delivery and there were no signs of defects, illness, pain, dehydration, hypoxia, acidaemia or other causes for the unresponsive behaviour.Clinical Findings and Treatment: Both calves were subjected to the thoracic squeeze technique, one at 6 hours and the other at 20 hours after delivery. A soft rope was looped around the thorax and gentle pressure was applied to the free end of the rope, squeezing the calf's chest for 20 minutes. Both calves exhibited a sleep-like state manifested by closed eyes, no body movements, slow breathing and a decrease in heart rate, for the entire squeezing period. When the rope was removed the calves woke up immediately, rose and walked towards the dam. When led to the dam's udder, the weaker calf began to suck. Both were reported, by the stockperson, to follow the dam and suck normally the following day.Clinical Relevance: Provided all other disease processes are excluded, very young calves that exhibit indifference to environmental stimuli and lack of affinity for the dam may be good candidates for application of the thoracic squeeze technique that has been demonstrated to have clinical efficacy in foals with neonatal maladjustment syndrome.


Subject(s)
Animals, Newborn , Cattle , Cesarean Section/veterinary , Restraint, Physical/veterinary , Animals , Animals, Newborn/physiology , Cattle/physiology , Cattle/surgery , Female , Pregnancy , Restraint, Physical/methods
3.
J Small Anim Pract ; 58(1): 3-9, 2017 Jan.
Article in English | MEDLINE | ID: mdl-28094859

ABSTRACT

OBJECTIVES: To investigate the association between hair nicotine concentration in cats and owner-reported exposure to environmental tobacco smoke. MATERIALS AND METHODS: Owner questionnaires documented exposure. Nicotine was extracted from hair by sonification in methanol followed by hydrophilic interaction chromatography with mass spectrometry. Relationships between hair nicotine concentration and owner-reported exposure were examined using hypothesis-testing statistics and receiver operating characteristic curve analysis. RESULTS: The hair nicotine concentration of reportedly exposed cats was significantly higher than unexposed cats and groups of cats with different levels of exposure had significantly different median hair nicotine concentrations corresponding to exposure. A hair nicotine concentration of 0·1 ng/mg had a specificity of 98% (95% confidence interval: 83 to 100) and a sensitivity of 69% (95% confidence interval: 54 to 84) for detecting environmental tobacco smoke exposure. Outdoors access, coat colour, urban or rural environment and length of time living with the owner were not obviously associated with hair nicotine concentration. CLINICAL SIGNIFICANCE: Feline hair nicotine concentration appears strongly associated with owner-reported environmental tobacco smoke exposure. Feline hair nicotine concentration could therefore be used as a biomarker for tobacco smoke exposure, allowing future studies to assess whether exposed cats have an increased risk of specific diseases.


Subject(s)
Cats , Hair/chemistry , Nicotine/analysis , Tobacco Smoke Pollution , Animals , Female , Male , Surveys and Questionnaires
4.
N Z Vet J ; 63(1): 31-6, 2015 Jan.
Article in English | MEDLINE | ID: mdl-25157557

ABSTRACT

The New Zealand dairy industry needs to meet public expectations regarding animal welfare in order to retain the freedom to operate and achieve market success. Three key orientations towards animal welfare assessment have been identified, namely biological functioning, affective state and natural living, the last two of which are more recent foci for societal concern. Biological functioning was the first and most-studied aspect of animal welfare and continues to be important, but now the contribution of affective state to animal well-being is emphasised much more. Natural living, or naturalness, has received relatively less attention from animal welfare science. It is proposed that increasing the use of naturalness as a contextual reference point for considering species-specific behavioural expressions of affective state will enhance its inclusion in animal welfare assessment. Nevertheless, all three orientations need to be considered in order to evaluate the significance of welfare research findings. On this basis, five key aspects of the New Zealand dairy industry that have been the subject of recent research, due to the risk of them not meeting public expectations, are highlighted and discussed. The aspects are provision of shade and shelter, meeting targets for body condition, provision of comfortable surfaces for rearing calves, and for adult cows while off pasture, and pain relief for disbudding of calves. Research evidence indicates that the industry guidelines on body condition score, if met, would satisfy public expectations across the three orientations to animal welfare, whereas further work is needed on the other aspects. It is concluded that considering these three orientations to animal welfare when planning research and then evaluating the outcomes will help to promote the market success of the dairy industry in New Zealand.


Subject(s)
Animal Husbandry/methods , Animal Welfare/standards , Cattle , Dairying/methods , Housing, Animal/standards , Animal Husbandry/standards , Animals , Research
5.
N Z Vet J ; 63(1): 24-30, 2015 Jan.
Article in English | MEDLINE | ID: mdl-25263963

ABSTRACT

Animal welfare is a state within the animal and a scientific perspective provides methodologies for evidence-based assessment of an animal's welfare. A simplistic definition of animal welfare might be how the animal feels now. Affective experiences including emotions, are subjective states so cannot be measured directly in animals, but there are informative indirect physiological and behavioural indices that can be cautiously used to interpret such experiences. This review enunciates several key science-based frameworks for understanding animal welfare. The biological functioning and affective state frameworks were initially seen as competing, but a recent more unified approach is that biological functioning is taken to include affective experiences and affective experiences are recognised as products of biological functioning, and knowledge of the dynamic interactions between the two is considered to be fundamental to managing and improving animal welfare. The value of these two frameworks in understanding the welfare of group-housed sows is reviewed. The majority of studies of the welfare of group-housed sows have employed the biological functioning framework to infer compromised sow welfare, on the basis that suboptimal biological functioning accompanies negative affective states such as sow hunger, pain, fear, helplessness, frustration and anger. Group housing facilitates social living, but group housing of gestating sows raises different welfare considerations to stall housing, such as high levels of aggression, injuries and stress, at least for several days after mixing, as well as subordinate sows being underfed due to competition at feeding. This paper highlights the challenges and potential opportunities for the continued improvement in sow management through well-focused research and multidisciplinary assessment of animal welfare. In future the management of sentient animals will require the promotion of positive affective experiences in animals and this is likely to be a major focus for animal welfare science activity in the early twenty-first century.


Subject(s)
Animal Husbandry/methods , Animal Husbandry/standards , Animal Welfare/standards , Behavior, Animal , Animals , Housing, Animal
6.
N Z Vet J ; 63(3): 131-40, 2015 May.
Article in English | MEDLINE | ID: mdl-25266360

ABSTRACT

This paper focuses on the development of behaviours that are critical for the survival of newborn and juvenile mammals of veterinary and wider biological interest. It provides an updated, integrated and comparative analysis of how postnatal maturation of sensory, motor and perceptual capacities support and constrain behavioural interactions between mammalian young and the mother, any littermates and the environment. Young that are neurologically exceptionally immature, moderately immature and mature at birth are compared, and include, for example, marsupial joeys, rodent pups and ruminant offspring. Mothers in these three groups exhibit distinctive patterns of birthing and postnatal care behaviours. To secure survival of the young, maternal care must compensate for behavioural inadequacies imposed by the limited sensory capacities the young possess at each stage. These sensory capacities develop in a predictable sequence in most mammals such that before birth the sequence progresses to an extent that parallels the degree of neurological maturity reached at birth. The extent of neurological maturity is likewise reflected in how long it takes after birth for the necessary brain circuit connectivity to develop sufficiently to support cortically based cognitive modulation of behaviour. This takes several months, days-to-weeks or minutes-to-hours in young that are, respectively, neurologically exceptionally immature, moderately immature, or mature at birth. Once achieved, cognitive awareness confers a high degree of behavioural flexibility that allows the young to respond more effectively to the unpredictability of their postnatal environments. It is shown that the onset of this cognitively based flexibility in the young of each group coincides with their first exposure to a variable environment that requires such behavioural flexibility.


Subject(s)
Animals, Newborn/growth & development , Behavior, Animal/physiology , Mammals/growth & development , Animals , Nervous System Physiological Phenomena
7.
N Z Vet J ; 63(1): 58-65, 2015 Jan.
Article in English | MEDLINE | ID: mdl-25238631

ABSTRACT

This review provides a scientific comment on the welfare of ruminants slaughtered by ventral-neck incision without stunning. Evidence is derived from studies of calves, sheep and goats. Reference is also made to findings in other mammals including humans. Pain is an inherently subjective experience and only indirect indices are available in animals. Neurophysiological tools are widely used in humans to assess pain and have demonstrated that electroencephalographic (EEG) variables correlate well with subjective evaluations of pain. These neurophysiological tools have also been applied in animal studies. In humans pain is associated with major cutting injuries and it is widely accepted that farm animals also experience pain due to such injuries. Overwhelming international scientific opinion has long been that slaughter by neck incision of conscious animals causes pain. A series of studies in calves demonstrated that slaughter by ventral-neck incision is likely to be perceived as painful. It is proposed that, as in cattle, non-stunned sheep and goats would experience pain in a similar manner. The precise assessment of the point after slaughter at which non-stunned animals become insensible remains a major methodological challenge. In sheep it is at least 2-8 seconds, but may be 8-20 seconds in duration. In cattle the mean duration is similar, but can commonly be extended to longer than 60 seconds with occasional instances of even greater durations. Taken together, these findings indicate that because the slaughter of cattle, sheep and goats by ventral-neck incision without prior stunning is likely to cause pain, this poses a risk to animal welfare.


Subject(s)
Abattoirs , Animal Welfare , Pain/veterinary , Ruminants , Animals
8.
N Z Vet J ; 63(1): 37-43, 2015 Jan.
Article in English | MEDLINE | ID: mdl-25147947

ABSTRACT

Many pest control activities have the potential to impact negatively on the welfare of animals, and animal welfare is an important consideration in the development, implementation and evaluation of ethically defensible vertebrate pest control. Thus, reliable and accurate methods for assessing welfare impacts are required. The Five Domains model provides a systematic method for identifying potential or actual welfare impacts associated with an event or situation in four physical or functional domains (nutrition, environment, health or functional status, behaviour) and one mental domain (overall mental or affective state). Here we evaluate the advantages and limitations of the Five Domains model for this purpose and illustrate them using specific examples from a recent assessment of the welfare impacts of poisons used to lethally control possums in New Zealand. The model has a number of advantages which include the following: the systematic identification of a wide range of impacts associated with a variety of control tools; the production of relative rankings of tools in terms of their welfare impacts; the easy incorporation of new information into assessments; and the highlighting of additional information needed. For example, a recent analysis of sodium fluoroacetate (1080) poisoning in possums revealed the need for more information on the period from the onset of clinical signs to the point at which consciousness is lost, as well as on the level of consciousness during or after the occurrence of muscle spasms and seizures. The model is also valuable because it clearly separates physical or functional and affective impacts, encourages more comprehensive consideration of negative affective experiences than has occurred in the past, and allows development and evaluation of targeted mitigation strategies. Caution must be used in interpreting and applying the outputs of the model, most importantly because relative rankings or grades are fundamentally qualitative in nature. Certain domains are more useful for evaluating impacts associated with slower/longer-acting tools than for faster-acting methods, and it may be easier to identify impacts in some domains than others. Overall, we conclude that the Five Domains model advances evaluation of the animal welfare impacts of vertebrate pest control methods, provided users are cognisant of its limitations.


Subject(s)
Animal Welfare , Pest Control , Vertebrates , Animals , Models, Biological
9.
N Z Vet J ; 63(1): 17-23, 2015 Jan.
Article in English | MEDLINE | ID: mdl-24875152

ABSTRACT

Developments in affective neuroscience and behavioural science during the last 10-15 years have together made it increasingly apparent that sentient animals are potentially much more sensitive to their environmental and social circumstances than was previously thought to be the case. It therefore seems likely that both the range and magnitude of welfare trade-offs that occur when animals are managed for human purposes have been underestimated even when minimalistic but arguably well-intentioned attempts have been made to maintain high levels of welfare. In light of these neuroscience-supported behaviour-based insights, the present review considers the extent to which the use of currently available reference standards might draw attention to these previously neglected areas of concern. It is concluded that the natural living orientation cannot provide an all-embracing or definitive welfare benchmark because of its primary focus on behavioural freedom. However assessments of this type, supported by neuroscience insights into behavioural motivation, may now carry greater weight when used to identify management practices that should be avoided, discontinued or substantially modified. Using currently accepted baseline standards as welfare reference points may result in small changes being accorded greater significance than would be the case if they were compared with higher standards, and this could slow the progress towards better levels of welfare. On the other hand, using "what animals want" as a reference standard has the appeal of focusing on the specific resources or conditions the animals would choose themselves and can potentially improve their welfare more quickly than the approach of making small increments above baseline standards. It is concluded that the cautious use of these approaches in different combinations could lead to recommendations that would more effectively promote positive welfare states in hitherto neglected areas of concern.


Subject(s)
Animal Husbandry , Animal Welfare/standards , Behavior, Animal , Animals
10.
N Z Vet J ; 63(1): 3-8, 2015 Jan.
Article in English | MEDLINE | ID: mdl-24875268

ABSTRACT

In line with an increasing emphasis on promoting positive welfare states in animals, this review extends previous accounts of how recent affective neuroscience observations may be used to identify and then to encourage animals to engage in reward-motivated behaviours. The terms affective states or affects are used to mean the subjective experiences, feelings or emotions that may motivate animals to behave in goal-directed ways and which may accompany success or failure to achieve those goals. These motivational affects may be positive, experienced as rewarding or pleasurable, or negative, experienced as aversive or punishing. There are two overall types: homeostasis-related negative affects that reflect an animal's internal physiological state, and situation-related positive or negative affects that reflect an animal's perception of its external circumstances. The major emphasis is on positive situation-related affects, in particular those that are potentially associated with exploration, feeding and animal-to-animal affiliative behaviours. The review introduces the new concept of positive affective engagement which represents the experience animals may have when they actively respond to motivations to engage in rewarding behaviours, and it incorporates all associated affects that are positive. For example, it would represent a state of engaged aliveness that may attend an animal's goal-directed, energised exploration of and interactions with a stimulus-rich environment. It also represents some states of equally energised, highly focused predatory stalking by carnivores or the focused and engaged foraging by herbivores when they are grazing in natural environments where food sources are abundant. Positive affective engagement may also be anticipated to accompany some aspects of reciprocated affiliative interactions between animals, the dedicated maternal nurturing and care of young, the joyfulness of rough-and-tumble play, and the eroticism and orgasmic pleasures of sexual activity. It is argued that highlighting the genetically pre-programmed, affectively positive impulses to engage in reward-motivated activities such as these, and the positive affects that may attend different facets of the process, draws attention to a wider spectrum of welfare enhancing experiences than has hitherto been considered to be important to animals. These neuroscience-supported observations strengthen many prior inferences made from predominantly behaviour-based investigations of animals' preferences, aversions and priorities, the associated development of successful environmental enrichments and the inclusion of these, where practicable, in more recent codes of practice or welfare.


Subject(s)
Animal Husbandry/methods , Animal Welfare , Housing, Animal/standards , Animals , Behavior, Animal
11.
N Z Vet J ; 63(1): 9-16, 2015 Jan.
Article in English | MEDLINE | ID: mdl-24875367

ABSTRACT

Affective neuroscience, incorporating neurophysiology and neuropsychology, is providing increasing evidence that certain behaviours of animals may be interpreted in terms of what they are intending to achieve, i.e. their goals. It is also providing evidence that allows inferences to be made about the affective contents of some goal-directed behaviours. These neuroscience-supported inferences are aligned with recommendations based on prior behaviour-based investigations of animals' preferences, aversions and priorities, and these observations together support the cautious use of particular behaviours to infer what the accompanying affects may be. In this review, therefore, some attention is given to negative affects and their relationships to poor animal welfare, but the primary focus is the positive affects animals may experience when they successfully engage in rewarding goal-directed behaviours, encapsulated in the concept of positive affective engagement. The review draws together reports of environment-focused and animal-to-animal interactive behaviours observed in a range of species and under diverse circumstances in order to illustrate the likely widespread occurrence of the positive affects that may accompany them. Particular consideration is given to affects that are potentially associated with some aspects of exploration and food acquisition in stimulus rich or impoverished environments, and to those that may be associated with aspects of the affiliative interactions of bonding or bond affirmation, maternal care, play and sexual activity. It is concluded that animals given the opportunity to engage in such activities may experience some positive affects. However, the intensity of an animal's experience of particular positive affects is likely to range from zero to very high because the associated behaviours occur intermittently, variation may occur during different phases of a goal-directed behaviour, and other positive or negative affects experienced at the same time may have greater impact. As good welfare is achieved both by minimising negative affects and promoting positive ones and as conscious sentient animals may be expected to have an interest in experiencing as little pain and as much pleasure as possible, it is argued that there is an ethical obligation to take practical steps to help them to achieve these outcomes. Such steps would include providing them with opportunities to express more behaviours that are associated with rewarding or satisfying experiences understood in terms of positive affective engagement.


Subject(s)
Animal Husbandry/methods , Animal Welfare , Behavior, Animal , Housing, Animal/standards , Animals
12.
N Z Vet J ; 63(1): 44-51, 2015 Jan.
Article in English | MEDLINE | ID: mdl-25004795

ABSTRACT

Breathlessness is a negative affective experience relating to respiration, the animal welfare significance of which has largely been underestimated in the veterinary and animal welfare sciences. In this review, we draw attention to the negative impact that breathlessness can have on the welfare of individual animals and to the wide range of situations in which mammals may experience breathlessness. At least three qualitatively distinct sensations of breathlessness are recognised in human medicine--respiratory effort, air hunger and chest tightness--and each of these reflects comparison by cerebral cortical processing of some combination of heightened ventilatory drive and/or impaired respiratory function. Each one occurs in a variety of pathological conditions and other situations, and more than one may be experienced simultaneously or in succession. However, the three qualities vary in terms of their unpleasantness, with air hunger reported to be the most unpleasant. We emphasise the important interplay among various primary stimuli to breathlessness and other physiological and pathophysiological conditions, as well as animal management practices. For example, asphyxia/drowning of healthy mammals or killing those with respiratory disease using gases containing high carbon dioxide tensions is likely to lead to severe air hunger, while brachycephalic obstructive airway syndrome in modern dog and cat breeds increases respiratory effort at rest and likely leads to air hunger during exertion. Using this information as a guide, we encourage animal welfare scientists, veterinarians, laboratory scientists, regulatory bodies and others involved in evaluations of animal welfare to consider whether or not breathlessness contributes to any compromise they may observe or wish to avoid or mitigate.


Subject(s)
Animal Welfare/standards , Dyspnea/veterinary , Animals , Respiratory Physiological Phenomena
13.
Vet Rec ; 175(4): 89, 2014 Jul 26.
Article in English | MEDLINE | ID: mdl-25013087

ABSTRACT

Accurate identification of mastitis-causing bacteria supports effective management and can be used to implement selective use of antimicrobials for treatment. The objectives of this study were to compare the results from a culture-based mastitis pathogen detection test kit ('VetoRapid', Vétoquinol) with standard laboratory culture and to evaluate the potential suitability of the test kit to inform a selective treatment programme. Overall 231 quarter milk samples from five UK dairy farms were collected. The sensitivity and specificity of the test kit for the identification of Escherichia coli, Staphylococcus aureus, coagulase-negative staphylococci, Streptococcus uberis and Enterococcus spp. ranged from 17 per cent to 84 per cent and 92 per cent to 98 per cent, respectively. In total, 23 of 68 clinical samples were assigned as meeting the requirement for antimicrobial treatment (Gram-positive organism cultured) according to standard culture results, with the test kit results having sensitivity and specificity of 91 per cent and 78 per cent, respectively. Several occurrences of misidentification are reported, including S. aureus being misidentified as coagulase-negative staphylococci and vice versa. The test kit provides rapid preliminary identification of five common causes of bovine mastitis under UK field conditions and is likely to be suitable for informing selective treatment of clinical mastitis caused by Gram-positive organisms.


Subject(s)
Bacteria/isolation & purification , Bacteriological Techniques/veterinary , Mastitis, Bovine/microbiology , Animals , Bacteriological Techniques/methods , Cattle , Culture Media , Female , Reproducibility of Results
14.
Rev Sci Tech ; 33(1): 21-32, 2014 Apr.
Article in English, French, Spanish | MEDLINE | ID: mdl-25000774
15.
Rev Sci Tech ; 33(1): 121-30, 2014 Apr.
Article in English | MEDLINE | ID: mdl-25000784

ABSTRACT

The process by which societies adapt to increasing knowledge about the mental and physical capacities of animals and the ways in which they are affected by human activities has been described as a journey. Different countries and regions are at various stages of this journey, and will take a unique path, depending on their specific social and cultural dynamics. However, all participants are unified by an increasing awareness of, and concern for, animal welfare. This journey has been characterised by a number of landmark events, one of which was the release of the Five Freedoms concept. Although aspirational and abstract, as it did not outline specific practical goals, nonetheless this concept became a catalyst for moving animal welfare thinking in a new direction, and set up a number of important targets for research. This eventually led to a key shift in thinking from a focus on biological functioning and resources, to ways of assessing welfare outcomes in terms of animals' experiences, i.e. their affective states. Behaviour science played an important role in the interpretation of animals' affective experiences, receiving compelling support from parallel studies in affective neuroscience. An important aspect of our understanding of animal welfare is that affective states can be negative or positive. Enabling animals to perform specific behaviours at key times when they are needed is central to the achievement of positive affective states. Another important event has been the development of practical ways to shift the spectrum of affective states towards a positive balance and their incorporation into welfare codes and regulations. The recent focus on positive affective states does not mean that negative experiences should be given less attention. In fact, in those countries that are at the early stages of the journey, improving function and productivity may be the most effective way to promote some important aspects of animal welfare. For example, alleviating pain is a useful entry point. Finally, it is important that the pace of the journey, in terms of public awareness and shifts in understanding, be supported by high-quality science that is rigorously assessed and validated in its practical application to the management of animal welfare.


Subject(s)
Animal Husbandry/standards , Animal Welfare/legislation & jurisprudence , Animal Welfare/standards , Animals , Humans , Public Policy , Quality of Life
19.
Science ; 341(6153): 1514-7, 2013 Sep 27.
Article in English | MEDLINE | ID: mdl-24030491

ABSTRACT

The global epidemic of multidrug-resistant Salmonella Typhimurium DT104 provides an important example, both in terms of the agent and its resistance, of a widely disseminated zoonotic pathogen. Here, with an unprecedented national collection of isolates collected contemporaneously from humans and animals and including a sample of internationally derived isolates, we have used whole-genome sequencing to dissect the phylogenetic associations of the bacterium and its antimicrobial resistance genes through the course of an epidemic. Contrary to current tenets supporting a single homogeneous epidemic, we demonstrate that the bacterium and its resistance genes were largely maintained within animal and human populations separately and that there was limited transmission, in either direction. We also show considerable variation in the resistance profiles, in contrast to the largely stable bacterial core genome, which emphasizes the critical importance of integrated genotypic data sets in understanding the ecology of bacterial zoonoses and antimicrobial resistance.


Subject(s)
Drug Resistance, Multiple, Bacterial/genetics , Host-Pathogen Interactions , Salmonella Infections, Animal/microbiology , Salmonella Infections/microbiology , Salmonella typhimurium/classification , Zoonoses/microbiology , Animals , Epidemics , Genome, Bacterial , Humans , Molecular Sequence Data , Phylogeny , Salmonella Infections/epidemiology , Salmonella Infections, Animal/epidemiology , Salmonella typhimurium/drug effects , Salmonella typhimurium/genetics
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