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    Genomic diversity of Campylobacter jejuni and Campylobacter coli isolates recovered from human and poultry in Australia and New Zealand, 2017 to 2019.
    (Microbiology Society, 2024-11-05) Cribb DM; Biggs PJ; McLure AT; Wallace RL; French NP; Glass K; Kirk MD
    We used genomic and epidemiological data to assess and compare the population structure and origins of Campylobacter, a major foodborne pathogen, in two neighbouring countries with strong trade and cultural links, similar poultry production systems and frequent movement of people and food products. The most common sequence types (STs) differed between Australia and New Zealand, with many unique to each country. Over half of all STs were represented by a single isolate. Multidrug-resistant (MDR) genotypes were detected in 0.8% of all samples, with no MDR isolates detected in poultry. Quinolone and tetracycline resistant ST6964 was prevalent in New Zealand (10.6% of C. jejuni). Closely related isolates suggested some similar food sources or contacts. We have shown that there is little genetic overlap in human and poultry STs of Campylobacter between the countries, which highlights that this common foodborne pathogen has domestic origins in Australia and New Zealand.
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    Population Structure and Antimicrobial Resistance in Campylobacter jejuni and C. coli Isolated from Humans with Diarrhea and from Poultry, East Africa.
    (Centers for Disease Control and Prevention, 2024-10) French NP; Thomas KM; Amani NB; Benschop J; Bigogo GM; Cleaveland S; Fayaz A; Hugho EA; Karimuribo ED; Kasagama E; Maganga R; Melubo ML; Midwinter AC; Mmbaga BT; Mosha VV; Mshana FI; Munyua P; Ochieng JB; Rogers L; Sindiyo E; Swai ES; Verani JR; Widdowson M-A; Wilkinson DA; Kazwala RR; Crump JA; Zadoks RN
    Campylobacteriosis and antimicrobial resistance (AMR) are global public health concerns. Africa is estimated to have the world's highest incidence of campylobacteriosis and a relatively high prevalence of AMR in Campylobacter spp. from humans and animals. Few studies have compared Campylobacter spp. isolated from humans and poultry in Africa using whole-genome sequencing and antimicrobial susceptibility testing. We explored the population structure and AMR of 178 Campylobacter isolates from East Africa, 81 from patients with diarrhea in Kenya and 97 from 56 poultry samples in Tanzania, collected during 2006-2017. Sequence type diversity was high in both poultry and human isolates, with some sequence types in common. The estimated prevalence of multidrug resistance, defined as resistance to >3 antimicrobial classes, was higher in poultry isolates (40.9%, 95% credible interval 23.6%-59.4%) than in human isolates (2.5%, 95% credible interval 0.3%-6.8%), underlining the importance of antimicrobial stewardship in livestock systems.
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    Characterization of two novel lytic bacteriophages having lysis potential against MDR avian pathogenic Escherichia coli strains of zoonotic potential.
    (Springer Nature Limited, 2023-06-20) Sattar S; Bailie M; Yaqoob A; Khanum S; Fatima K; Altaf AURB; Ahmed I; Shah STA; Munawar J; Zehra QA; Daud S; Arshad A; Imdad K; Javed S; Tariq A; Bostan N; Altermann E
    Avian pathogenic E. coli (APEC) is associated with local and systemic infections in poultry, ducks, turkeys, and many other avian species, leading to heavy economical losses. These APEC strains are presumed to possess zoonotic potential due to common virulence markers that can cause urinary tract infections in humans. The prophylactic use of antibiotics in the poultry sector has led to the rapid emergence of Multiple Drug Resistant (MDR) APEC strains that act as reservoirs and put human populations at risk. This calls for consideration of alternative strategies to decrease the bacterial load. Here, we report isolation, preliminary characterization, and genome analysis of two novel lytic phage species (Escherichia phage SKA49 and Escherichia phage SKA64) against MDR strain of APEC, QZJM25. Both phages were able to keep QZJM25 growth significantly less than the untreated bacterial control for approximately 18 h. The host range was tested against Escherichia coli strains of poultry and human UTI infections. SKA49 had a broader host range in contrast to SKA64. Both phages were stable at 37 °C only. Their genome analysis indicated their safety as no recombination, integration and host virulence genes were identified. Both these phages can be good candidates for control of APEC strains based on their lysis potential.
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    Genome Analysis and Therapeutic Evaluation of a Novel Lytic Bacteriophage of Salmonella Typhimurium: Suggestive of a New Genus in the Subfamily Vequintavirinae.
    (MDPI (Basel, Switzerland), 2022-01-25) Sattar S; Ullah I; Khanum S; Bailie M; Shamsi B; Ahmed I; Abbas Shah T; Javed S; Ghafoor A; Pervaiz A; Sohail F; Imdad K; Tariq A; Bostan N; Ali I; Altermann E; Griffiths M; Anany H
    Salmonella Typhimurium, a foodborne pathogen, is a major concern for food safety. Its MDR serovars of animal origin pose a serious threat to the human population. Phage therapy can be an alternative for the treatment of such MDR Salmonella serovars. In this study, we report on detailed genome analyses of a novel Salmonella phage (Salmonella-Phage-SSBI34) and evaluate its therapeutic potential. The phage was evaluated for latent time, burst size, host range, and bacterial growth reduction in liquid cultures. The phage stability was examined at various pH levels and temperatures. The genome analysis (141.095 Kb) indicated that its nucleotide sequence is novel, as it exhibited only 1-7% DNA coverage. The phage genome features 44% GC content, and 234 putative open reading frames were predicted. The genome was predicted to encode for 28 structural proteins and 40 enzymes related to nucleotide metabolism, DNA modification, and protein synthesis. Further, the genome features 11 tRNA genes for 10 different amino acids, indicating alternate codon usage, and hosts a unique hydrolase for bacterial lysis. This study provides new insights into the subfamily Vequintavirinae, of which SSBI34 may represent a new genus.
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    Transmission dynamics of an antimicrobial resistant Campylobacter jejuni lineage in New Zealand’s commercial poultry network
    (Elsevier B.V, 2021-12) Greening SS; Zhang J; Midwinter AC; Wilkinson DA; Fayaz A; Williamson DA; Anderson MJ; Gates MC; French NP
    Understanding the relative contribution of different between-farm transmission pathways is essential in guiding recommendations for mitigating disease spread. This study investigated the association between contact pathways linking poultry farms in New Zealand and the genetic relatedness of antimicrobial resistant Campylobacter jejuni Sequence Type 6964 (ST-6964), with the aim of identifying the most likely contact pathways that contributed to its rapid spread across the industry. Whole-genome sequencing was performed on 167C. jejuni ST-6964 isolates sampled from across 30 New Zealand commercial poultry enterprises. The genetic relatedness between isolates was determined using whole genome multilocus sequence typing (wgMLST). Permutational multivariate analysis of variance and distance-based linear models were used to explore the strength of the relationship between pairwise genetic associations among the C. jejuni isolates and each of several pairwise distance matrices, indicating either the geographical distance between farms or the network distance of transportation vehicles. Overall, a significant association was found between the pairwise genetic relatedness of the C. jejuni isolates and the parent company, the road distance and the network distance of transporting feed vehicles. This result suggests that the transportation of feed within the commercial poultry industry as well as other local contacts between flocks, such as the movements of personnel, may have played a significant role in the spread of C. jejuni. However, further information on the historical contact patterns between farms is needed to fully characterise the risk of these pathways and to understand how they could be targeted to reduce the spread of C. jejuni.
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    Trends in feed evaluation for poultry with emphasis on in vitro techniques
    (Elsevier B.V. on behalf of KeAi Communications Co. Ltd, 2021-06) Zaefarian F; Cowieson AJ; Pontoppidan K; Abdollahi MR; Ravindran V
    Accurate knowledge of the actual nutritional value of individual feed ingredients and complete diets is critical for efficient and sustainable animal production. For this reason, feed evaluation has always been in the forefront of nutritional research. Feed evaluation for poultry involves several approaches that include chemical analysis, table values, prediction equations, near-infrared reflectance spectroscopy, in vivo data and in vitro digestion techniques. Among these, the use of animals (in vivo) is the most valuable to gain information on nutrient utilization and is more predictive of bird performance. However, in vivo methods are expensive, laborious and time-consuming. It is therefore important to establish in vitro methods that are reliable, rapid and practical to assess the nutritional quality of feed ingredients or complete diets. Accuracy of the technique is crucial, as poor prediction will have a negative impact on bird performance and, increase feed cost and environmental issues. In this review, the relevance and importance of feed evaluation in poultry nutrition will be highlighted and the various approaches to evaluate the feed value of feed ingredients or complete diets will be discussed. Trends in and practical limitations encountered in feed evaluation science, with emphasis on in vitro digestion techniques, will be discussed.
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    Studies on the measurement of calcium digestibility in raw materials for poultry and of digestible calcium requirement of broiler starters : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Animal Science (Poultry Nutrition) at Massey University, Palmerston North, Manawatu, New Zealand
    (Massey University, 2021) David, Laura Shiromi
    The measurement of calcium (Ca) digestibility in feed ingredients for poultry is receiving increasing attention because of recent interest in formulating diets based on digestible phosphorous (P) and the close relationship between these two minerals in their absorption and post absorptive utilisation. Data on the ileal Ca digestibility of Ca sources and factors influencing Ca digestibility in poultry are scant. The current thesis presents follow-up studies of the previous work conducted at Massey University. The Ca digestibility values of Ca sources determined in the thesis, along with previous published data, were then used to develop dietary treatments to assess the digestible Ca requirement of broiler starters. The first study reported in Chapter 3 was conducted to examine the effect of basal diet composition on true ileal Ca digestibility of four Ca sources namely, limestone, meat and bone meal (MBM), monocalcium phosphate (MCP) and dicalcium phosphate (DCP) in broiler chickens. Two basal diets, namely a maize-based diet and a maize-starch-based purified diet, with each Ca source were tested. The results showed that the average true ileal Ca digestibility was higher in the maize-based diet (0.46) than that in the purified diet (0.37). True ileal Ca digestibility of limestone, MBM, MCP and DCP were determined to be 0.51, 0.41, 0.43 and 0.32, respectively. In the study reported in Chapter 4, the effect of dietary indicator-type and dietary adaptation length on the apparent ileal Ca digestibility of limestone were evaluated. In Experiment 1, the use of two indicators namely, titanium dioxide and acid insoluble ash (Celite) were compared and the findings showed that the ileal Ca digestibility was unaffected by dietary indicator. In Experiment 2, four dietary adaptation lengths namely, 24, 72, 120 and 168 hours were examined and it was found that the Ca digestibility was unchanged between 72 and 120 hours but decreased at 168 hours of adaptation length. The third study, presented in Chapter 5, was conducted to measure the influence of age (7, 14, 21, 28, 35 and 42 days post-hatch) on the Ca digestibility of limestone for broiler chickens. The findings revealed that the apparent ileal Ca digestibility coefficients were linearly decreased from day 7 to day 42. The ileal Ca digestibility coefficients were determined to be 0.51, 0.53, 0.36, 0.34, 0.41 and 0.27 at days 7, 14, 21, 28, 35 and 42, respectively. A secondary objective of this study was to examine the influence of dietary crude protein concentration (79 and 153 g/kg) on the apparent ileal Ca digestibility at 21 days of age. It was found the apparent ileal Ca digestibility was not influenced by dietary protein concentrations. The studies reported in Chapter 6 were conducted to measure the influence of phytase doses (0, 500 and 2000 FTU/kg) on the Ca and P digestibility of soybean meal (SBM) and canola meal (CM) in broiler starters (Experiment 1) and finishers (Experiment 2). True ileal Ca digestibility coefficients of SBM and CM, with no supplemental phytase, were determined to be 0.51 and 0.53, respectively, for broiler starters and 0.33 and 0.22, respectively, for broiler finishers. True ileal P digestibility coefficients of maize-SBM diet and maize-CM diet, with no phytase were determined to be 0.89 and 0.66, respectively, for broiler starters and 0.82 and 0.57, respectively, for broiler finishers. Microbial phytase increased the true ileal digestibility of Ca and P in maize-SBM diet and maize-CM diet, but the effect was more pronounced for the maize-CM diet. Superdosing of phytase (2000 FTU/kg) increased the Ca digestibility in CM and SBM by two-fold compared to the normal phytase dose (500 FTU/kg). The studies reported in Chapter 7 were conducted to determine the ileal Ca digestibility coefficients of two limestone sources in broilers and layers. The results showed that, in both sources, the apparent ileal Ca digestibility of limestone was found to be higher in laying hens (0.62 and 0.70) compared to broilers (0.50 and 0.43). The findings indicated that laying hens absorb Ca more efficiently than broilers which may be attributed to their high demand of Ca for eggshell formation. Using Ca digestibility values of Ca sources measured in this thesis work and previous published data, a growth study (Chapter 8) was conducted to estimate the standardised ileal digestible (SID) Ca requirement for 1 to 10 day-old broilers fed different dietary concentrations of both SID Ca (3.3, 3.9, 4.4, 5.0 and 5.5 g/kg) and SID P (4, 5 and 6 g/kg). Based on response surface models, the growth performance, bone mineralisation and mineral utilisation of broiler starters were found to be optimised at 5 g/kg SID P concentration. The concentrations of SID Ca that maximised body weight gain, tibia ash, tibia Ca, tibia P and toe ash were estimated to be 3.32, 4.51, 4.72, 4.36 and 4.78 g/kg, respectively, which corresponds to SID Ca to SID P ratios of 0.66, 0.90, 0.94, 0.87 and 0.96, respectively. Bone mineralisation required more SID Ca than for growth. Most of the findings reported in this thesis are novel and contribute to the advancement of current knowledge on the measurement of ileal Ca digestibility in poultry and the factors influencing Ca digestibility. The array of factors examined were hitherto unexplored and included the effects of basal diet type, dietary adaptation length, broiler age, phytase dose, Ca source and bird type (broilers vs. layers). Another notable contribution was to establish the requirements of digestible Ca, digestible P and the ratio of digestible Ca to digestible P for broiler starters (1-10-day old).
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    Influence of feed processing and enzyme supplementation on performance, nutrient utilisation and gut morphology of poultry fed barley-based diets : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Poultry Nutrition at Massey University, Palmerston North, Manawatu, New Zealand
    (Massey University, 2020) Perera, Wellawattage Nipuna Udayani
    The first experiment (Chapter 3) determined the metabolisable energy and standardised ileal digestible amino acids of two barley cultivars (NSH [normal starch hulled barley] and WSHL [waxy starch hull-less barley]) and wheat for broilers. These values were used to formulate the experimental diets in subsequent experiments that evaluated the optimum barley inclusion rate in wheat-based diets (Chapters 4 and 5), optimum barley particle size (Chapter 6) and conditioning temperature (CT; Chapter 7), and potential interaction of carbohydrases with each processing parameter. In Chapter 3, wheat and WSHL had the highest and lowest metabolisable energy and digestible amino acid contents, respectively, with NSH being intermediate. Supplemental carbohydrases increased the energy utilisation with a pronounced effect in WSHL. Data reported in Chapter 4 showed that optimum inclusion level of NSH was 283 g/kg of diet. Nutrient utilisation linearly improved with increasing inclusions of NSH. Carbohydrases improved feed per gain (F/G) and nutrient utilisation. Chapter 5 suggested that WSHL could be safely included up to 260 g/kg in a wheat-based diet with no adverse effect on growth performance. Carbohydrases improved the F/G and, starch and energy utilisation. In Chapter 6, particle size effect was preserved after pelleting and, coarse barley and carbohydrases improved the F/G and nutrient utilisation. The combination of carbohydrase and phytase produced no further improvements in nutrient utilisation. The final experiment (Chapter 7) demonstrated that better pellet quality achieved by increasing CT to 88 °C failed to ameliorate the negative impacts of high CT on nutrient utilisation and broiler performance. Carbohydrases improved weight gain, F/G and, starch and energy utilisation. The lack of interaction between the carbohydrases and CT indicated that carbohydrase had similar efficacy at each CT. The primary finding of this thesis research was that if cultivar-specific values for metabolisable energy and digestible amino acids are used in feed formulations, barley has the potential to substitute up to 50% of wheat in broiler diets. Coarse particle size (8.0 mm) and conditioning the diets up to 74 °C is recommended for the tested barley type. Supplemental carbohydrases improved the feeding value of barley for broilers.
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    The role of dietary calcium in the control of egg production : a thesis ... for the degree of Master of Agricultural Science at Massey University
    (Massey University, 1975) Gibbins, Alan Michael
    Dietary calcium restriotion is studied as a method of controlling egg production. Attempts have been made to delay the onset of egg production in the fowl by feeding pre-laying diets deficient in calcium. Calcium restriction had no apparent effect on sexual development and did not delay the time· of first oviposition. Low calcium diets were used at a later date to halt egg production firstly just after peak production and secondly towards the end of the first laying year. Egg production was depressed markedly but never completely ceased, and remained at a low level until calcium restrictions were lifted whereupon a rapid rise returned egg production to levels comparable to egg production rates of non calcium restricted control hens. Comparisons between egg production, egg weight, shell weight and a measure of shell quality (shell weight per unit surface area of egg) revealed trends towards improved shell production and shell quality following calcium restriction but little else. There was only a small number of significant differences. Egg production pauses induced by low dietary calcium were thought to be unsatisfactory as substitutes for force moulting. Calcium restriction caused declines in food consumption and body weight. While food consumption returned to levels equivalent to food consumption of non calcium restricted hens after calcium restriction, body weight in general did not. Calculations of the calcium loss from the body of calcium restricted hens via egg·shell production show that extremely severe depletion occurs unless egg prvduction is stopped or at least egg shell production is stopped. Such depletion of calcium has greatest effects on the skeleton and damage to the bones, particularly of the legs, may result. This is a condition which may predispose to a paralytic condition characteristic of extreme calcium deficiency.
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    Measurement of true ileal phosphorus digestibility in feed ingredients for poultry : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Poultry Science at Institute of Veterinary, Animal and Biomedical Sciences (IVABS), Massey University, Palmerston North, New Zealand
    (Massey University, 2014) Mutucumarana, Ruvini Kamalika
    Global interest in improving the utilisation of phosphorus (P) by poultry has recently increased due to concerns over environmental pollution through excess P excretion, depletion of non-renewable inorganic phosphate deposits, and increasing price of inorganic phosphate supplements. Use of a sound criterion, preferably based on P digestibility, to assess P availability is needed to enable greater efficiency of utilisation of dietary P. No established methodology is currently available to measure the true digestible P contents in common feed ingredients for poultry. The first experiment of this thesis (Chapter 3) investigated the effects of dietary calcium (Ca) concentrations (6, 9 and 12 g/kg) on the digestibility of P, Ca, nitrogen, fat and starch in different intestinal segments and on the apparent metabolisable energy of diets in young broiler chickens. The results showed that the digestion of P and Ca was completed by upper ileum and jejunum, respectively. The site of digestion of P and nitrogen was found to shift depending on the dietary Ca concentrations. The digestibility coefficients of P in low, normal and high Ca diets at the lower ileum were determined to be 0.417, 0.379 and 0.325, respectively. The overall data showed that increasing dietary Ca concentrations negatively influenced the digestion of P, nitrogen and fat, but had no effect on those of Ca, starch and apparent metabolisable energy. The second experiment (Chapter 4) was conducted to determine endogenous losses of P and Ca in broiler chickens. The data showed that the ileal endogenous P losses in birds differed depending on the methodology employed. The ileal endogenous flow of P in birds fed P-free, gelatin-based and casein-based diets were 25, 104 and 438 mg/kg dry matter intake (DMI), respectively. Ileal endogenous flow of Ca in birds fed casein-based diet was estimated to be 321 mg/kg DMI. The next three experiments (Chapters 5, 6 and 7) investigated the potential usefulness of regression method to evaluate true ileal P digestibility of seven feed ingredients. True ileal P digestibility coefficients of maize, canola meal, wheat, sorghum, soybean meal and maize-distiller‟s dried grains with solubles for broiler chickens were determined to be 0.676, 0.469, 0.464, 0.331, 0.798 and 0.727, respectively. For plant-based ingredients, the determined true digestible P values were consistently higher than corresponding non-phytate P values (Maize, 1.72 vs. 0.75; canola meal, 4.55 vs. 2.82; wheat, 1.49 vs. 1.11; sorghum, 0.78 vs. 0.55; soybean meal, 5.16 vs. 2.15; maize-distiller‟s dried grains with solubles, 5.94 vs. 4.36 g/kg, as fed ii basis, respectively). Phytate P in maize (54.25%), soybean meal (69.7%) and maize- distiller‟s dried grains with solubles (41.5%) were well digested by broilers compared to canola meal (25.2%), wheat (18.1%) and sorghum (13.0%). True ileal P digestibility coefficients of three meat and bone meal (MBM) samples ranged from 0.420 to 0.693. Total and true digestible P contents of three MBM samples (MBM-1, MBM-2 and MBM-3) were determined to be 37.5 and 26.0; 60.2 and 36.6; and 59.8 and 25.1 g/kg, as fed basis, respectively, suggesting that P in MBM is not highly digestible. The overall data suggested that the use of regression approach to estimate true ileal P digestibility in feed ingredients has number of limitations. Overestimation as a result of using Ca- and P-deficient diets and the negative endogenous P losses observed for some ingredients (canola meal, sorghum and MBM-3) were main concerns. Negative ileal endogenous P losses were also shown to be associated with low true ileal P digestibility in these ingredients. In the final experiment (Chapter 8), two regression-based methodologies were compared for the measurement of true ileal P digestibility in maize and soybean meal. The results showed that the methodology influenced P digestibility in maize and soybean meal. The use of assay diets containing a narrow Ca:total P ratio yielded higher P digestibility for both ingredients. In this thesis research, the regression method was used to determine true ileal P digestibility of ingredients, but this approach suffers from several drawbacks. The data reported in this thesis also demonstrated that high dietary Ca concentrations were detrimental to the digestibility of nutrients, particularly of P, nitrogen and fat.